After taking the oath of office, Sun Yat-sen sent telegrams to the leaders of all provinces, requesting them to elect and send new senators to establish the National Assembly of the Republic of China. Then the provisional government organizational guidelines and the provisional law of the Republic were declared as the basic law of the country by the Assembly.

The provisional government was in a very weak position. The southern provinces of China had declared independence from the Qing dynasty, but most of the northern provinces had not. Moreover, the provisional government did not have military forces of its own, and its control over elements of the New Army that had mutinied was limited, and there were still significant forces which had not declared against the Qing.

The major issue before the provisional government was gaining the support of Yuan Shikai, the man in charge of the Beiyang Army, the military of northern China. After promising Yuan the presidency of the new Republic, Yuan sided with the revolution and forced the emperor to abdicate. Later, Yuan proclaimed himself emperor and afterwards opposition snowballed against Yuan's dictatorial methods. In 1913 Sun led an unsuccessful revolt against Yuan, and he was forced to seek asylum in Japan, where he reorganized the Kuomintang. He married Soong Ching-ling, one of the Soong sisters, in Japan on October 25, 1915, without divorcing his first wife Lu Muzhen due to opposition from the Chinese community. Lu pleaded with him to take Soong as a concubine but this was also unacceptable to Sun's Christian ethics.