With the development of human technology and the progress of human society, virtual reality technology has provided technical support for cultural transmission and exchange, enabling virtual technology to better fulfill the cultural dissemination and social education values of museums. To improve the construction of virtual museums and enhance user experience within them, this study designs a virtual museum navigation system based on the concept of interactive design, offering technical support for better human–computer interaction (HCI) functionality in virtual museums. Firstly, grounded in HCI theory, the study analyzes the design of navigation systems in virtual museums that enhance user experience, as well as key design elements for HCI functionality in virtual museums. Based on the concept of HCI and centered around user needs, this study constructs a design strategy for the virtual museum navigation system, including a clear definition of the navigation interface and the mode of HCI in virtual museums. Experimental tests have shown that the navigation system based on HCI design can effectively conduct emotional analysis of users’ positions and poses. The optimization system for user experience in virtual museums, designed through the concept of HCI, provides design methods and strategies with greater practical application value for enhancing user experience in virtual museums in subsequent design practices.