The museum's primary goal is to provide a well-curated collection of specimens to be used for research and education by the communities to which it belongs: the University of Puget Sound, the Puget Sound region, and, in a broad sense, the world. Museums have an ever-increasing responsibility for the conservation of specimens as animal and plant populations are threatened by human activities, and the Puget Sound Museum of Natural History is one of the region's significant repositories for these specimens. Furthermore, museum collections serve as the primary sources of information about both spatial and temporal aspects of biodiversity anywhere in the world. To accomplish this, the museum will continue to enhance its collections, especially of regional animals and plants, and to search for orphaned collections to preserve.

A secondary goal of the museum is to demonstrate and educate about the value of natural-history museums.