He fought in the Battle of the Boyne, Aghrim, and at the capitulation of Limerick, serving under William III of England and under James II of Ireland.
Jones was admitted an associate freeholder under the original patent of Oyster Bay, granted by Governor Andros, on 29 September 1677.
Lord Cornbury, the Governor of New York, commissioned him to be Captain of Militia in Queens County on 20 October 1702.
His tombstone, made of hard red sandstone of Rhode Island, bore an inscription written by himself (with original spelling preserved): Here Lyes Interred The Body of Major Thomas Jones, who came from Strabane, in the Kingdom of Ireland, Settled here, and Died, December, 1713.
He became judge of Queens County in 1734, and in 1763 was the 2nd Justice of the Supreme Court of New York, where he sat for ten years.
He became Recorder of the City of New York and Judge of the Supreme Court, which later office he held until the close of the Revolutionary War, when he was forced to leave the country for England.