Lord St Germans married Lady Jemima Cornwallis (24 December 1803, Brome, Suffolk – 2 July 1856, Dover Street, London), daughter of Charles Cornwallis, 2nd Marquess Cornwallis, at St James Church, Westminster, on 2 September 1824. They had six sons and two daughters:
Lady Louisa Susan Cornwallis Eliot (17 December 1825 – 15 January 1911), married Walter Ponsonby, 7th Earl of Bessborough and was the mother of Edward Ponsonby, 8th Earl of Bessborough.
Edward John Cornwallis Eliot, Lord Eliot (2 April 1827 – 26 November 1864), born London, educated at Eton from 1839–1843, matriculated at Christ Church, Oxford on 21 October 1844, styled Lord Eliot from January 1845, commissioned a Cornet and Sub-lieutenant, 1st Regiment of Life Guards and subsequently Captain of that Regiment, 1852, died unmarried at Port Eliot.
Captain Hon. Granville Charles Cornwallis Eliot (9 September 1828 – 5 November 1854), officer Coldstream Guards, killed at the Battle of Inkerman.
William Gordon Cornwallis Eliot, 4th Earl of St Germans (14 December 1829 – 19 March 1881)
Hon. Ernest Cornwallis Eliot (28 April 1831 – 23 January 1832)
Lady Elizabeth Harriet Cornwallis Eliot (September 1833 – 16 March 1835)
Henry Cornwallis Eliot, 5th Earl of St Germans (11 February 1835 – 24 September 1911)
Colonel Hon. Charles George Cornwallis Eliot, CVO (16 October 1839 – 22 May 1901), courtier and soldier, succeeded Alpin McGregor as a Gentleman Usher Daily Waiter to Queen Victoria in 1899, married on 26 October 1865 Constance Rhiannon Guest, daughter of Sir John Josiah Guest, Bt and Lady Charlotte Guest.
Lord St Germans died at St Germans on 7 October 1877, aged 79.