In the following years Morse helped to audit and supervise the China Merchants' Steam Navigation Company, a joint venture between Chinese officials and merchants. He worked with Sheng Xuanhuai, but ran into trouble negotiating the political currents. Upon his resignation from the company in 1877, he was reassigned to Shanghai, where he supervised the Statistical Department. 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 and Nan were sent to Pakhoi (Mandarin: Beihai), on the north coast of the Gulf of Tonkin, in 1889, and then on a two-year leave in the United States. Their next posting was to Tamsui in Taiwan, where he was an important witness to the Japanese invasion of Taiwan in 1895. He then served in Pakhoi once more, Youzhou, Hunan, and Hankow. Poor health forced him to take leave from 1900–1903, but he returned to the Customs Service to head the Statistical Service from 1904 to 1908. He retired from the Customs Service in 1908.