Sir Thomas Cotton, 2nd Baronet, of Conington (1594 – 13 May 1662) was an English politician and heir to the Cottonian Library.
He was the only surviving child of Sir Robert Cotton, 1st Baronet, of Connington and Elizabeth Brocas.
On 23 July 1631, the council ordered the catalogue to be continued; but in September Sir Thomas announced that it had been again interrupted, and begged to be allowed to retain possession of the books.
He moved the greater part of the library in 1650 to a villa at Stratton, Bedfordshire, which belonged to his son's wife.
Their second son, Robert, was Member of Parliament for Cambridgeshire, was knighted, was commissioner of the post office, and was friendly with John Evelyn.