Sun Yat-sen took office on 10 September, with Li Liejun as chief of staff, Li Fulin as commander-in-chief of the army, Xu Chongzhi as staff officer, and Chen Jiongming as commander-in-chief of the First Army, and the military government was established.

On 10 April 1918, the Extraordinary Congress, adhering to the wishes of the Southwestern Warlords, passed the "Republic of China Military Government Organization Outline Amendment" and decided to reorganize the military government and change the general marshal system to the presidential collegiate system; Sun Yat-sen resolutely opposed this decision.

On 4 May 1918, Sun Yat-sen angrily resigned to the Extraordinary Congress and energized him to expose the crime of the Southwestern warlord's sabotage of the Constitutional Protection Movement.

In the mid-1920s, the Guangzhou military government appeared to have infighting, and the British-backed Guangxi and Dian groups fought for power.

Sun Yat-sen returned to Guangzhou on 28 November and resumed his post as General Marshal and President of the Army and Navy, and reorganized the southern military government to continue the constitutional protection movement.