Morse was at first stationed in Shanghai, where he studied the northern dialect, Mandarin, for an hour each day before breakfast, and then served in Beijing.
When posted to the London office of the Customs Service, he met Annie Josephine Welsford – "Nan" – who had been born in Brooklyn to British parents.
On the couple's subsequent posting to Tianjin, Nan took an almost instant dislike to China and the Chinese, though it is not clear how this affected her husband's attitudes.
Morse was involved under Li Hongzhang's direction, in the diplomacy surrounding the Sino-French War of 1885 for which he received the Order of the Double Dragon, third division, second class.
In the North China Branch of the Royal Asiatic Society, he found himself one of some two hundred and fifty members, most of whom worked for the Customs Service, and soon became one of the most productive.
He traveled frequently to the United States, and kept up relations with his Harvard classmates, including Charles Franklin Thwing, president of Western Reserve University.
Articles in magazines and journals included "A Short Lived Republic," which recounted his resistance to the 1895 takeover of Taiwan by Japan and the attempt to establish an independent nation.
He had first contemplated the study in 1919, and was able to carry it out only because the India Office allowed him to remove the record books and ledgers and work on them at home.
He scrupulously summarized and edited some two hundred years of trade and commercial relations of the Company, giving historians a lasting documentary.
He wrote that although the older scholar lived through the decades of foreign imperialism and the collapse of the Qing empire, his historical work "avoids the obtrusive chauvinism of the Western treaty port community of that period."
Fairbank noted that Morse "records the criticisms.... but gives little indication of the more positive side of the Confucian tradition, including its effort to maintain the ideals of loyalty and public service, and its capacity for reform."