In March 1612, he married Elizabeth Home (d. 19 August 1633), daughter of George Home, 1st Earl of Dunbar. They had nine children:
James Howard, 3rd Earl of Suffolk (c.1620–1689)
Thomas Howard
Catherine Howard (d. 1650), married first George Stewart, 9th Seigneur d'Aubigny (d. 1642), second James Livingston, 1st Earl of Newburgh
Elizabeth Howard (d. 11 March 1705), married on 1 October 1642 Algernon Percy, 10th Earl of Northumberland
Margaret Howard, married Roger Boyle, 1st Earl of Orrery
George Howard, 4th Earl of Suffolk (1625–1691)
Henry Howard, 5th Earl of Suffolk (1627–1709)
Anne Howard, married Thomas Walsingham
Frances Howard (d. October 1677), married Sir Edward Villiers (d. 1689)