The institution began its activities in the 1920s as the Herzen Local Nature Museum. Over its nearly century-long history, the exhibition has changed its name multiple times, but its main functions have remained unchanged: collecting, studying, and popularizing knowledge about the nature of the Vologda region, as well as observing changes in fauna and flora after the creation of the Rybinsk Reservoir.

Today, the Nature Museum boasts a rich collection of minerals, rocks, and fossils. Its total area is 500 square meters. In addition to exhibition halls, there is a small hall for classes and lessons intended for schoolchildren and students. The museum features two permanent exhibitions: "Forest Motifs" and "Journey into the World of Fossils." The first exhibition is dedicated to the natural wealth of Cherepovets and its surroundings, as well as the development of local flora and fauna.

The museum's collection includes about 30,000 exhibits displayed in various exhibitions. Ancient fossils are presented in the "Journey into the World of Fossils" section. The formation of the funds for this exhibition began back in 1907 when the remains of extinct animals were discovered during the construction of a pier on the Yagorba River. In the 1940s to 1970s, the collection was actively replenished during the construction of the metallurgical plant. Many mammoth bones were found in nearby quarries and construction pits. Museum staff continue to conduct expeditions, enriching the collections with new valuable materials.

A separate large section is dedicated to a collection of photographs reflecting the beauty of Russian nature. It houses works by renowned photographers such as V. N. Mikhailov, M. V. Berezovsky, and N. D. Shkurupadsky.