First wife

Clifton's first wife was Isabel Herbert (died c. November 1457), widow of William Scott (died 5 February 1434) of Brabourne, Kent, and daughter of Vincent Herbert (alias Finche) of Netherfield, Sussex by his wife Isabel Cralle, daughter and coheiress of Robert Cralle. Their two daughters were:^[4]

• Isabel Clifton, who in 1459 married John Jerningham (died 1503) of Somerleyton, Suffolk, by whom she had two sons and several daughters, including:^[4][5][6][7]
  • Sir Edward Jerningham (died 1515), who married firstly Margaret Bedingfield (d. 24 March 1504), and secondly Mary Scrope (d. 25 August 1548).
  • Sir Richard Jerningham (died 1525/6), Gentleman of the Privy Chamber to King Henry VIII, who married Anne Sapcote (d. 14 March 1559), who survived him and remarried to John Russell, 1st Earl of Bedford, by whom she was the mother of Francis Russell, 2nd Earl of Bedford.
  • Margaret (or Mary) Jerningham, who married Thomas Stanhope of Rampton and was the grandmother of Anne Seymour, Duchess of Somerset (née Anne Stanhope).
• Joan Clifton, who married John Digges of Digges Court in Barham, Kent and was the grandmother of the scientist, Leonard Digges.^[8][9]

Second wife

Clifton's second marriage, before 20 March 1463, was to Maud Stanhope (died 30 August 1497), widow firstly of Robert Willoughby, 6th Baron Willoughby de Eresby (died 1452), and secondly of Sir Thomas Neville (killed at Battle of Wakefield 30 December 1460), second son of Richard Neville, 5th Earl of Salisbury, executed at Pontefract on 31 December 1460 after the Battle of Wakefield. Maud Stanhope was the daughter of Sir Richard Stanhope (died 1436) of Rampton, Nottinghamshire by his second wife, Maud Cromwell (died 30 August 1497), daughter of Ralph Cromwell, 2nd Baron Cromwell (died c. 2 May 1417). Maud Stanhope was the niece and coheiress of Ralph de Cromwell, 3rd Baron Cromwell (d. 4 January 1456), and the heiress of her sister, Joan Stanhope (died 10 March 1490), who had married firstly Sir Humphrey Bourchier (died 1471), slain at the Battle of Barnet on 14 April 1471, and secondly Sir Robert Radfcliffe of Hunstanton, Norfolk.

There were no children from Clifton's second marriage, and after his death his widow, Maud Stanhope, alleged that he had 'wasted and destroyed' more than £1000 worth of jewels, plate and household goods which she brought to the marriage as her dowry. She died 30 August 1497, and was buried in the Collegiate Church at Tattershall, Lincolnshire.;^{[10][11][12][13]}