It is housed in an old building constructed in 1907 located at the foot of Cerro de las Campanas.

This building served as a penitentiary and was built by the prisoners themselves, many of whom were from the Yaqui indigenous group, using stones extracted from the same hill. The cells and corridors are still preserved to this day.

The museum has 18 rooms where a collection of pieces related to paleontology, archaeology, ethnography, and history are exhibited. Notable items include a Teotihuacan stone serpent, armor and coins from the 16th century, a collection of 19th-century weapons, and a representation of the Yaqui indigenous dance.

The museum also features a space for temporary exhibitions and a library.