Doughty was born on August 19, 1843, and named for his father, Rev. Charles Montagu Doughty, Squire of Theberton, Suffolk. His mother was the former Frederica Beaumont, daughter of the Honourable and Reverend Frederick Hotham, Rector of Dennington, Prebendary of Rochester, and son of Baron Hotham. Thwarted in his first ambition, Doughty turned to an early interest in geology with new vigour. He devoted himself to the study of Suffolk chalk and by 1862 he was able to communicate on the subject of flint implements from Hoxne with the British Association meeting at Cambridge. From 1865 until 1870 Doughty studied both at London and at the Bodleian Library at Oxford, not geology or the natural sciences, but early English literature. He felt that he had discharged his patriotic duty in this matter by first offering the British Museum the opportunity to buy his impressions: they had been 'refused rather contemptuously by Dr. Birch', he wrote to Hogarth.