 On 13 March 1804, Malthus married Harriet, daughter of John Eckersall of Claverton House, near Bath.They had a son and two daughters.His first born Henry became vicar of Effingham, Surrey in 1835 and of Donnington, Sussex in 1837; he married Sofia Otter (1807–1889), daughter of Bishop William Otter and died in August 1882, aged 76.