On 12 April 1647, he married Hon. Anne Bayning, a daughter of the 2nd Viscount Bayning. Anne died in 1659 and Aubrey married Diana Kirke and they had one child, Lady Diana de Vere, who married King Charles II's illegitimate son, the Duke of St Albans.
He was the last Vere Earl of Oxford, one of the longest-lived peerages. The first Vere earl had received his title from the Empress Matilda in 1141.