The history of educational work on the study of the nature of the Kostroma region is closely intertwined with the overall development of industry and public life in the early 20th century. In particular, at the provincial agricultural, handicraft, and industrial exhibition dedicated to the 300th anniversary of the Romanov dynasty, an exhibition showcasing the natural riches of the region was presented. Significant contributions to the creation of future collections were made by members of the Kostroma Scientific Society for the Study of the Local Region, founded in 1912. The society had biological, geophysical, and ethnological stations, a geological laboratory, and actively published the results of its research, creating a network of district and volost cells. After the October Revolution of 1917, the society transferred its collections to the local history museum, established on the basis of the Romanov Museum.

In 1926, the museum was enriched by a unique collection bequeathed by amateur entomologist Ivan Mikhailovich Rubin, who was an active member of the society and a former member of the Kostroma District Court. Rubin's collection, which includes over four thousand species of insects from various parts of the world, has significant educational and informative value. In 1958, with the establishment of the Kostroma State Historical and Architectural Museum-Reserve in the walls of the former Holy Trinity Ipatiev Monastery, a nature department was founded. Its creation is associated with the names of the first museum director Maria Mikhailovna Orekhova and taxidermist Vladimir Andreevich Tyak. Local artists and hunters, such as Boris Ivanovich Myasnikov and Albert Ivanovich Yeryomin, participated in the creation of museum exhibitions. The diorama principle was used in the design of the halls. In the early 1960s, a fire destroyed the best dioramas of the museum, such as "Wolf Attack on Elk" and "Snowy Owl." They were restored in 1964 and 1965. The exhibition "Flora and Fauna" was organized by seasons. In 1965, the updated nature department became the most popular in the museum-reserve. In 1966, the famous entomological collection of I. M. Rubin was prepared for display. In 1969, the exhibition "Origin of Man" was created, and in 1970, the exhibition on the topic "Geology of the Region" and the exhibition "Origin of Life on Earth." In 1972, the creation of exhibitions on the topics "Geographical Characteristics, Waters, Soils, and Mineral Resources of the Kostroma Region" was completed. In 2001, due to the transfer of the buildings of the New City of the Ipatiev Monastery to the Kostroma Diocese of the Russian Orthodox Church, the nature department was transformed into an independent Nature Museum of the Kostroma Region and moved to a separate building on Moloknaya Hill. The exhibition was disrupted, and many dioramas were destroyed. The first exhibition in the new building was "Entomological Collection of I.M. Rubin." In 2002, the exhibition "Hunting Trophies" opened, followed by the exhibition "Birds and Animals of the Kostroma Region." The restoration of the "Winter" hall began with the diorama "Lynx Hunting," and the exhibition "Wolf Attack on Elk" was restored only in 2009. In 2006, the restoration of the "Spring" hall and the creation of the memorial hall of V.A. Tyak were underway. In 2013, new dioramas appeared in the "Spring" hall, such as "Spring Water Body" and "Migratory Birds." In 2014, the exhibition "Insectarium" opened.