Firstly, on 6 March 1650, he married Elizabeth Henshaw (baptised 29 April 1621 – c.1654) at St Bartholomew-the-Great in London, a sister of the alchemist Thomas Henshaw, with issue including:
Lionel Duckett (1652–1693), who was also a member of parliament for Calne.[4][1]
Secondly, about 1655, he remarried, as a widower, the widow Anne Chapman née Knight (died 1667), with issue including:
Jane Duckett (1657–1713)
Three short-lived sons
Thirdly, about September 1669 (licence: 13 September 1669, Bristol), he remarried, as a widower, Margaret Moore (d. 1694), a daughter of Sir Henry Moore, 2nd Baronet, of Fawley, Berkshire. There were no documented children from this marriage.
Duckett died on 1 November 1686[2] at his home in Calne, Wiltshire, at the age of 62. He was buried on 5 November 1686. His will was executed by his widow, Margaret, with probate on 3 January 1687.