At the beginning of the 20th century, the Museum of Mongolia was established as a scientific center under the Institute of Scripts Writing. In 1921-1923, the researchers who worked at the institute focused on the preparatory work required for the establishment of the museum, collecting the natural, historical, and cultural objects of Mongolia, and writing records and descriptions of the museum.

The collection of museum exhibits was formed in many ways, one of which included artifacts and objects of the Russian-Soviet and American exploration teams who worked in our country.

Before the opening of the first museum, P.K. Kozlov's exhibition of antiquities made a valuable contribution to the enrichment of the collection and became an example of the way of organizing museum exhibitions. This exhibition was viewed with great interest by the Mongolians, and a year later, it was enriched with the artifacts of the expedition led by the famous tourist Roy Andrews of the Natural History Museum of the United States.

In 1926, according to the decision of the government to expand the State Museum to the Bogd Khan’s Winter Palace, the rooms of the Palace were repaired and painted for organizing the museum, and the exhibits were displayed in various categories.

The State Museum renovated its exhibits again in 1940-1941, significantly changing the display and sequence of historical and natural exhibits, adding new artifacts, and this was the second renovation of the museum with the goals of enriching its artifacts in the fields of history, ethnology, art, and natural objects and expanding the local studies. Therefore, since 1940, it has been called the "Museum of Local Studies".

In 1954-1956, the State Museum, which was in Bogd Palace, was moved to a new building being built on Engels Street, the building and the equipment for preparing exhibits, the development of explanatory research, the preparation of new equipment and displays were successfully completed in parallel, and the museum was opened in the middle of 1956. The museum was then called the "State Central Museum".

In the 1960s and 1990s, Bogd Khan Palace Museum, Choijin-Church Museum of Religious History and Art, Erdene-zuu, and Amarbayasgalant were branches of the State Central Museum.

According to the Order No. 214 of the Chairman of the Culture and Arts Development Committee under the Government of the Mongolian People’s Republic dated August 23, 1991, the Natural History Museum was established in the building of the State Central Museum, and Mr. Perlee Altangerel was appointed as the Director, and Mr. Erdembat Puntsag as the Deputy Director.

In 1993, the Deputy Director Mr. Erdembat Puntsag was appointed as the Director. For 12 years, Mr. Erdembat Puntsag managed the establishment of the Natural History Museum independently from the beginning, enriching the collections, training the staff, and taking the exhibition arrangement to a new level.

From 2005 to 2021, Mr. N. Zorigtbaatar served as the Director of the Museum. During this period, the museum signed cooperation agreements with many museums such as the Science History Museum of South Korea, Hwaseong and Jeju Natural History Museums, Changjo Natural History Museum and Institutes of Biology and Biotechnology, Azabu University of Japan and Toyoko Museum, Beijing and Tianjin Natural History Museums of PRC, Belgian and French Science Museums, Milan Natural History Museum of Italy, the Novosibirsk Museums of Russian Federation etc. to exchange work experience, train staff, organize exhibitions, and cooperate in the fields of research and analysis.

According to Resolution No. 281 of the Government of Mongolia dated July 3, 2019, "On Combining the Museums", the Central Dinosaur Museum was dissolved and merged into the Natural History Museum.

Mr. Budbayar Ishgen was appointed as the Director of the Museum in 2022, and the activities of the Museum have expanded, in 2022-2023, the permanent exhibition halls were renovated and reorganized to serve the audience.