The museum was founded on December 29, 1870, when the Ural Society of Naturalists (USN) opened in Yekaterinburg. The initiator of the society's creation was French language teacher Onisim Egorovich Kler. Initially, the society was located in a boys' gymnasium, where the local history museum was established. Its collection included the first gifts: books, minerals, and a preserved snake. At first, the exhibits were stored with the donors or members of the USN, but in August 1871, the society was allocated two rooms in the building of the mining department.

The museum began to form zoological, mineralogical, paleontological, and botanical collections. In 1873, a numismatic collection appeared, as well as an archaeological one, thanks to a find by student Alexei Bryukhanov. In 1874, the museum received a collection of iron and copper samples from I. N. Privalov, which became the basis for the industrial department. That same year, the museum moved to a more spacious location, but the exhibition opportunities remained limited.

In 1887, the USN organized the Siberian-Ural Scientific and Industrial Exhibition in Yekaterinburg, which significantly increased the museum's funds. By January 1, 1888, the collection numbered 13,064 items, of which the zoological collection was the largest. The museum opened for visitors on December 27, 1888, and in its first year, it was visited by 1,293 people.

In 1891, the USN received the patronage of Grand Duke Mikhail Nikolaevich, which allowed it to receive an annual subsidy of 2,000 rubles starting in 1895. In 1901, a collegial management system was introduced in the museum, and 10 departments were created. By 1912, the collections had increased to 28,891 items.

On December 29, 1895, a fire occurred in the museum, which severely damaged the collections. This event prompted the creation of a fund for the construction of a new building. In 1911, the foundation for the new museum building was laid, but due to World War I, the project remained unrealized.

By 1920, the museum had 42,020 items and 11 departments, and in 1924, it was visited by 21,420 people. In 1925, the museum became the Ural Regional State Museum, leading to the opening of new museums in Sverdlovsk.

In 1941, the museum was closed, and its premises were used for other needs. In 1946, the museum received the building of the Ascension Church for exhibitions. In 1960, it was transferred the building of the Alexander Nevsky Cathedral, where the funds and scientific library were located.

In 1978, the museum was transformed into a museum association with branches. In 1987, the museum was given a building at 46 Malysheva Street, where an exhibition on the history of the Urals in the 20th century opened.

In 1991, buildings previously belonging to the museum were transferred to the Church, and the museum received new premises. In 1994, the Museum of the History of Fruit Growing in the Middle Urals opened. In 2001, the updated Nature Museum opened at 4 Gorky Street.

In 2013, the Center for Innovative Museum Technologies was created based on the museum. As of 2016, the museum's collections include 725,588 exhibits, and the annual number of visitors is about 270,000.