The planning office of the museum was established in April of 1981. The first phase of construction was completed in January of 1986. On January 16, 1987, the museum’s organizational bylaws were passed by the Legislative Yuan and promulgated by the President on February 20 of that year. The revised organizational structure passed the third reading in the Legislative Yuan on March 21, 1997 and includes eight departments and four offices. They are the Zoology, Botany, Geology, Anthropology, Collection Management, Science Education, Exhibits and Information departments, as well as the Secretariat, Personnel Office, Accounting Office and Government Ethics Office.
To meet the requirement of the government’s organization restructuring, the museum was reorganized in January 2013 to consist of six departments, four offices and one administration center. They are departments of Biology, Geology, Anthropology, Science Education, Exhibits, and the Department of Operation, Visitor Service and Information Management. Four offices include the Secretariat, Personnel, Accounting, and Government Ethics. In addition, the Administration Center of Natural Science Education Parks is responsible for the operation of three parks. Currently, the museum has a total staff of 339.