The organization was founded in January 1930 in Shanghai. After the Law on Civic Organization and the Medical Practitioners Law was legislated in 1942 and 1943, TMA got the First License issued from the Social Department of the government. Based on the instruction of the Social Department of the government in 1948, the Fifth National Congress met in Chongqing in October 1943 was revised as the First National Congress and the Sixth National Congress met in Nanjing in March 1948 was revised as the Second National Congress after the registration in 1943.

After the government's retreat to Taiwan in 1949, the reelection of officers became impossible that the organization was unable to carry on the regular operation. In July 1967 and July 1979, Taipei City and Kaohsiung City were elevated to municipalities directly under the jurisdiction of Executive Yuan. Considering both domestic and international change, the government and the physicians revised the Medical Practitioners Law, amended the 41-1 article, which is: “Owing to great changes now besetting the nation, when the national medical organizations are unable to convene their national delegates' congresses, they may, upon approval of the government agencies, assemble as many of their members as possible and conduct supplementary elections of their directors and supervisors.”

Accordingly, On 4 September 1979 the organization convened the Second Congress's first conference of the directors and supervisors as well as the delegates from the membership organizations, making up through supplementary elections the shortfall in numbers of directors and supervisors, thereby restoring the organization to regular operation.

In 1991, the Period of National Mobilization for Suppression of the Communist Rebellion came to an end; as a result, the 41-1 article of the Medical Practitioner's Law was deleted. The congress held in May 1992 is as the 3rd National Congress and all the members of directors and supervisors who were elected from China were retired. In July 1997, the National Assembly enacted the 9th Amendment to the Constitution that vacated the provincial structure. In January 2002, the 31st article of the Medical Practitioner's Law was revised that the provincial medical organization was vacated. Thus, TMA was re-organized according to the revised Medical Practitioner's Law.