Multiscale virtual environments (MSVEs) allow the integration of elements and environments at different scale levels into a unified space, which facilitates researchers’ perception, understanding, and experimental research of complex geospatial spaces. Although there have been several methods for achieving multiscale effects in virtual environments (VEs), they cannot assist users in constructing more complete spatial cognitive maps and presenting multiscale information efficiently. This study proposes a hierarchical-structure-based MSVE construction method, which can effectively integrate multiscale information and ensure that the richness of details of information is gradually enhanced with the progression of the hierarchical structure. In addition, a spatial navigation study is conducted, considering the relationship between users’ perspective changes and spatial cognition, and the effects of users’ perspective changes on their spatial cognition in an MSVE are explored. A multiscale virtual wetland environment covering four levels is constructed to conduct a case study of a virtual environment of a wetland of Poyang Lake. The research results show that the proposed method is feasible. Moreover, the spatial navigation based on the change in the hierarchical perspective is in line with the spatial cognitive habits of users, which can satisfy the cognitive needs of users from the macro-region to specific wetland landscapes.