The museum in Novorossiysk was founded on July 7, 1916, at the initiative of the vice-governor of the Black Sea province, L.A. Senko-Popovsky, and was originally called the Museum of Nature and History of the Black Sea Coast of the Caucasus. Its exhibition was solemnly opened on December 27, 1916. The main sources of funding for the museum were voluntary donations from people supporting its development.

After the establishment of Soviet power in Novorossiysk, the museum came under the management of the City Council. Its work involved director V.E. Meyerhold and writer F.V. Gladkov. From 1921 to 1933, the museum was headed by Georgy Fedoseevich Chaikovsky, who authored numerous articles on the antiquities of the region and participated in archaeological congresses in the North Caucasus. The museum was recognized as a scientific and artistic institution and included in the list of state museums, but it was funded from local sources, with an obligation to report on its activities annually.

By the beginning of the Great Patriotic War, the Novorossiysk Local History Museum had become a major scientific and educational institution in Kuban, with about 7,000 exhibits and a library containing 44,500 books. However, during the war, the museum suffered significant losses: buildings were destroyed, collections were looted, and the library was destroyed. Only part of the archaeological collections and documents were evacuated to Tbilisi thanks to the efforts of teacher G.P. Aleksanyan.

The restoration of the museum began in January 1944 under the leadership of director V.M. Mironova. By May 1944, a new premises was found, and on November 7, the museum reopened to visitors. Its exhibition included both surviving and new exhibits. By the end of 1947, the museum's collections numbered 4,435 exhibits, and the library had 200 books.

In 1952, the museum returned to part of its pre-war building and opened a new exhibition in 1953. In 1954, excavations of the Raevsky settlement began under the direction of archaeologist V.D. Blavatsky. These studies were continued in the 60s and 70s by Nadezhda Anisimovna Onaiko. Today, archaeological research is conducted in collaboration with the Institute of Archaeology of the Russian Academy of Sciences.

In 1958, the museum moved to a new location, where a new exhibition and a diorama triptych dedicated to the liberation of Novorossiysk in 1943 opened in 1960. In 1971, a memorial exhibition dedicated to the weapons and technology of the Great Patriotic War was opened.

In 1977, the museum was transferred a house where N. Ostrovsky lived and part of a historical building for an exhibition hall. This event was significant for the cultural life of the city. Over the years, the museum's collections have significantly increased and now number over 150,000 items. Archaeological collections continue to be replenished thanks to annual expeditions.

In 1982, the State Museum of the 18th Army was established, and in 1987, based on it and other objects, the Novorossiysk State Historical Museum-Reserve was created. Today, it is the second largest museum in Kuban, playing an important role in the patriotic and aesthetic education of the younger generation.