On 13 March 1804, Malthus married Harriet, daughter of John Eckersall of Claverton House, near Bath. They had a son and two daughters. His firstborn, son 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. His middle child, Emily, died in 1885, outliving her parents and siblings. The youngest, Lucille, died unmarried and childless in 1825, months before her 18th birthday.