In 1933, most of the museum's collection was evacuated. The evacuation was forced by the threat of Japanese invasion.

 After the end of World War II, the collection was returned to the museum in Nanjing, but after the Communist victory in the Chinese Civil War, the government decided to send the collection to Taiwan.

Of the 13,491 boxes of evacuated artifacts, 2,972 are now in the National Palace Museum in Taipei. More than 8,000 boxes have been returned to Beijing, but 2,221 remain in storage at the Nanijng Museum.