Throughout the course of the People's Republic of China's history, the position that effectively reigned as the Commander-in-Chief of the Armed Forces changed from time to time. During some periods, it was not exactly clear who was the supreme commander of the People's Liberation Army.
From 1949-1969, the "official" Commander-in-Chief of the Armed Forces was the President of the People's Republic of China, who was also the head of the National Security Council. However, a similar command structure inside the communist party known as the Central Military Commission was indeed responsible for the PLA. The Commission was headed by a Chairman, Mao Zedong. Vice-Chairs included Liu Shaoqi, which from 1959-1969, was the President. Eventhough the President was the "official" Supreme commander of the military, it nonetheless was a subordinate of the CMC Chairman.
From 1969 to 1978, the head of the military was the Chairman of the Central Committee of the CPC. This gave constitutional power to the head of a party.
From 1978 onwards, the Commander-in-Chief was the Chairman of the CMC. This position, however did not always give the person entitled the top command as was the case with Hua Guofeng. Deng Xiaoping was able to effectively control the military as the Chief of Staff of the PLA from 1978-1980.