Taiwan Garrison Command was commanded by a three-star general officer and contained both officers or enlisted personnel from the Army, Marine Corps, Military Police, Political Warfare, or Intelligence Bureau; and members from the National Police Agency of the Ministry of the Interior, as well as civilian recruits from other colleges after special training.

Although officially a military division, Taiwan Garrison Command actually functioned as a secret police organization.

On 20 May 1949, Chen Cheng, in his capacity as commanding general for the province and its military governor, declared martial law in Taiwan.

The Southeast Military Governor Office, headed by Chen Cheng, was responsible for the defense of four provinces: Jiangsu, Zhejiang, Fujian and Taiwan; and was directly responsible for the systematic killing of thousands of Taiwanese social elites, as part of what became known as the February 28 incident.

The Taiwan Garrison Command was involved in the 1980 murder of lawyer and opposition politician Lin I-hsiung and his family.

[7] On 30 April 1991, President Lee Teng-hui declared the termination of the Period of Communist Rebellion and Taiwan Garrison Command again lost its other lawful justification.