It has been 600 years since the Marquis of Guide's Palace and the King of Han's Palace were constructed in the early Ming Dynasty, on the site now occupied by the Presidential Palace. During the Qing Dynasty, the Liangjiang Governor-General Yamen was located here, and in 1853, the Palace of the Taiping Heavenly Kingdom was built here as the official residence of the Heavenly King, Hong Xiuquan.

Following the establishment of the Republic of China, Dr. Sun Yatsen took the oath of Provisional President in this compound on January 1, 1912 and it was used as the office of the Nationalist Government after April 1927. During the years of the Anti-Japanese War, the Japanese army and Chinese puppet regime occupied the buildings here. After Japan's defeat, the Nationalist Government returned to Nanjing in 1946 and in 1948 the compound became the Presidential Palace.

There were two wings in the Presidential Palace. The Executive Yuan(Council) of the Nationalist Government was located in the East Wing and its main military authorities in the West Wing.

On April 23, 1949, the People's Liberation Army occupied the Presidential Palace, from which a new age in Chinese history began.

The Presidential Palace has been used as the official place of Party and government organizations since 1950.

This museum was planned in to 1998, and already it has begun to take shape in 2003 after five years of meticulous planning and painstaking construction. This museum covers an area of ninety thousand square meters in total and it is divided into three areas. There are sites of the Nationalist Government and the Presidential Palace in the central area. The office of the Provisional President, its secretariat, the Department of Staffs and the West Garden are located in the western section. The site of the Executive Yuan building, as well as the East Garden are situated to the east.

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