Thomas was a son of Rev. Thomas Stoughton and his wife Katherine, baptized at Naughton, Suffolk, England, on 23 January 1592/3. He apparently was their second son to be named Thomas; the records show that a child recorded as Thomas Sloughe, child of Thomas & Katherine, was baptized on 9 July 1588.
Thomas Stoughton and Elizabeth (his first wife) married in England. She was either
Elizabeth Tompson, married 5 May 1612 in Great Totham, Essex. Elizabeth ____
Elizabeth _____ Stoughton was the mother of his six or seven children.
Elizabeth must have died before 1635, either in Massachusetts Bay, after emigrating with Thomas and her children in the 1630 Winthrop fleet
OR shortly before 29 December 1627 in Aller, Somerset , possibly as a results of complications of pregnancy.
Thomas Stoughton married as his second wife, Margaret Barrett Huntington, widow of Simon Huntington, in Dorchester in 1635.  (In a letter of December 1634 to his stepfather Rev. John Stoughton, James Cudworth of Scituate reported that "my uncle Thomas is to be married shortly, to a widow (of Simon Huntington) that has good means and has five children."
Emigration to Massachusetts Bay - A Family Affair
1630 -- Thomas, with (perhaps) his wife Elizabeth Montpeson Stoughton, and (definitely) their children (Thomas Jr., Katherine, and perhaps more); Thomas's brother Israel and Israel's wife, Elizabeth; and Thomas' and Israel's sister, Judith Stoughton Denman Smead and her son, William Smead Jr., and her daughter Mary Denman, sailed on the ship "Mary and John" from England to the Massachusetts Bay Colony as part of the 1630 John Winthrop's Fleet. They settled at Dorchester. 
The following family members  are listed as sailing with Winthrop's Fleet:
Smead, ____ From Coggeshall, Essex. No further record. Probably died soon.
Smead, Judith (Stoughton) Wife of ____Smead. Sister of Israel Stoughton (Savage).
Smead, William Son of Mrs. Judith Smead (Savage)."
Stoughton, Israel (Dorchester) From Coggeshall, Essex. Was opposed to the rule of Winthrop and disfranchised for writing an heretical book. Returned to England and fought under Cromwell in the Civil War, with the rank of Lieutenant Colonel in Rainsborough's regiment. (Savage). He died 1644 at Lincoln.
Stoughton, Elizabeth Wife of Israel.
Stoughton, Thomas (Dorchester) From Coggeshall, Essex. Brother of Israel. Constable 28 Sept 1630. Applied freeman 19 Oct 1630 (M.C.R., I, 80); Freeman 18 May 1631 (ibid., 366). Married to Mrs. Margaret Huntington, widow of Simon Huntington, in 1635. He removed to Windsor, Conn[ecticut Colony] where he died in 1642.
Stoughton, _____ Wife of Thomas (Savage).
Israel and Thomas Stoughton were two of the 25 out of 247 heads of families "of a social rank above that of yeoman or husbandmen." The early records gave Israel and Thomas "the prefix of 'Mr.'" 
1630 or 1635 - 1639 -- Thomas's and Israel's sister, Judith Stoughton Denman Smead, and her children arrived at Salem then settled at Dorchester. . Other sources say they also sailed with Winthrop's Fleet in 1630. 
Activities in Dorchester, Massachusetts Bay
September 28, 1630 -- appointed Constable of Dorchester  But soon after, he was fined 5 pounds and sentenced to be jailed until his fine was paid, for marrying Clement Briggs and Joane Allen. Thomas did not pay the fine, nor was he jailed, and in 1638 the fine was rescinded.
Nevertheless, Thomas was regarded as a man of "Prominence, property & social distinction," and was referred to as "ancient,' which signified Ensign or standard bearer in a military company.
October 19, 1630 -- Thomas requested to become a freeman "(M.C.R., I, page 80)" 
May 18, 1631 -- Thomas became a freeman in Dorchester. 
May 18, 1631 - 1634 -- Thomas served on the General Court [Dorchester or Massachusetts Bay Colony?]
1634 -- Thomas was one of 10 men chosen to "order the affairs of the [Dorchester] plantation."
1635 -- in the Dorchester records, reference was made to \"Mr. Thomas Stoughton's lot\" .
Religious Disputes, and Migration to Connecticut
1635 - Religious dissension came to a boil in Dorchester. Followers of Rev. Thomas Hooker who disagreed with Governor John Winthrop migrated to Connecticut. Thomas, along with Henry Wolcott, Mr. Newberry, Roger Ludlow, and John Mason, were appointed to establish a new settlement on the Connecticut River, near the Plymouth Trading Post. These men defrayed most of the expenses of the migration from Dorchester to Windsor, and the new plantation/settlement of Windsor, Connecticut.
Activities in Windsor, Connecticut Colony
1636 -- Thomas was chosen to establish the boundaries of Windsor.
Thomas Stoughton "was deputy in 39 and 43 -- juror in 42 -- lieutenant in 40." 
1638 - 1648 -- For 11 consecutive years, Thomas was elected to represent Windsor in the Connecticut General Court
1639 - listed as a church member in Windsor, Connecticut 
1640 - on 11 January , Thomas Stoughton's holdings included a home lot with fifty-two acres of meadow, and a meadow of twenty-four acre,s" in an exchange with Thomas Gunne. 
1646 & 1651 - Thomas wrote, to John Winthrop, letters that were lengthy religious treatises, indicating that while he had no university education, he had learned quite a lot elsewhere.
Thomas died at Windsor, Connecticut Colony in March 1661-2 
Children With first wife, Elizabeth Montpeson or Thomson
i ELIZABETH, bp. Great Coggeshall 28 February 1612/3; d. soon.
ii ELIZABETH, bp. Great Coggeshall 20 March 1613/4; bur. there 15 July 1619.
iii ANNA, bp. Great Coggeshall 29 October 1615; no further record.
iv SARAH, bp. Great Coggeshall 10 January 1618/9; d. Windsor 1652 [Grant 82]. 
v KATHERINE, bp. Great Coggeshall 12 May 1622; m. Hartford 18 January 1649/50 John Wilcock [HaVR 608].
vi THOMAS, bp. Aller, Somerset, 21 August 1625; m. Windsor 30 November 1655 Mary Wadsworth [CTVR 42; Grant 65]."}
Property Transfers in Windsor
Apparently references Thomas Stoughton's Will and land grant to his son Thomas Stoughton, Jr., 1624-1684. (Unclear if Israel Stoughton 1626-1644 is included.)
"11th January, 1640. Thomas Stoughton, Sr., hath granted to him from the Plantation an Homelott whereon his Dwelling House now stands, wch together wth the Additions and Meadow adjoyning conteynes in yt 52 acres ..., 25 acres of Meadow ... Also, towards Plmo Mead 69 acres more or less,...(See Stiles's History of Windsor, Vol. II, Page 722)
We learn from tradition that the brothers, Thomas and Israel, were accompanied to New England by their father, Thomas, Senior. Thomas the Elder, as he is designated on the Land Rec. of Windsor, in a deed date 14 July, 1645, makes over to "Thomas, my son," all his ppty in W. except his home lott, well court, and court before the house, and orchard, evidently reserved for his own use. Afterwards Thomas Stoughton the Elder sold to Thomas the younger his dwelling house and outhouses, orchard and courts, formerly exempted, provided the said Thomas the younger shall afford convenient maintenance to the said Thomas his father, and his mother-in-law, that is, the former widow Huntington, during the time of their lives, and in case Mr. Stoughton dyes first, then to all ( ) his mother-in-law the third part of a hundred pounds which the said particulars were prized at, or to allow the said convenient maintenance with himself during her life (being her choice), provided she live with the said Thomas, otherwise not. "
↑ Research note: Sarah Stoughton is generally thought to have survived childhood and emigrated to Massachusetts Bay with her parents and younger siblings. However, in view of the history of the Stoughtons it is highly unlikely that she was the Sarah Hollander who married John Denman in Long Island, New Netherlands and had a family there. Better parents are needed for Hollander-1, and more research is needed to find well-sourced life facts for Sarah Stoughton.
↑ A DIGEST OF THE EARLY CONNECTICUT PROBATE RECORDS.1635 to 1700, Windsor Lands, Page 16, Sec. State's office. Vol. I
Names of such as took the Oath of Freemen -- 18 May 1631. Accessed by Michael Boynton on May 17, 2016 at 2:00 AM. 
Catalogue of the names of the first Puritan settlers of the colony of Connecticut, A, [database on-line]. Provo, UT: Ancestry.com Operations Inc, 2004. Original data: Hinman, Royal Ralph,. A catalogue of the names of the first Puritan settlers of the colony of Connecticut : with the time of their arrival in the colony and their standing in society, together with their place of residence, as far as can be discovered by the records /c collected from the state and town records by R. R. Hinman.. Hartford: Printed by E. Gleason, 1988.
DIGEST OF THE EARLY CONNECTICUT PROBATE RECORDS.1635 to 1700, Am Windsor Lands, Page 16, Sec. State's office. Vol. I, Ancestry.com. Hartford, Connecticut Probate Records, 1639-1700 [database on-line]. Provo, UT, USA: Ancestry.com Operations Inc, 2000. Original data: A Digest of the Early Connecticut Probate Records, Hartford District, 1635-1700. Vol. I. n.p., 1906.
Winthrop Fleet of 1630, The: an Account of the Vessels, the Voyage, the Passengers and Their English Homes, from Original Authorities, by Charles Edward Banks; Boston: Houghton Mifflin, 1930. 119p. Reprinted by Genealogical Publishing Co., Baltimore, 1961. Repr. 1983. Reprinted 2003. Pages 92 - 93. http://files.usgwarchives.net/ma/mastate/winthropfleet.txt
Savage, James. A Genealogical Dictionary of the First Settlers of New England: Showing Three Generations of Those Who Came Before May, 1692, on the Basis of Farmer's Register. (Boston: Little, Brown, and Co, 1860-1862), 4:213.