In this paper we present the design and implementation of a comparative experiment to study the differences in spatial cognition between head-mounted virtual reality geographic information systems (VRGIS) and desktop monitor-based virtual geographic environments, collect virtual travel behavior data from two groups of participants and explore the differences in spatial cognition. The collected virtual travel behavioral data include subjects' self-drawn cognitive maps, movement trajectories and viewing trajectories. Then the differences in spatial cognitive performance, forgetting scores and viewing trajectories are analyzed. The following conclusions are drawn:①The head-mounted VRGIS group scores significantly higher than desktop monitor-based group in three levels of spatial cognition including spatial feature perception, spatial object cognition and spatial pattern cognition. ②The two groups do not show a significant difference in forgetting scores. ③The average rate of change in horizontal viewing direction is significantly greater in the head-mounted VRGIS group than in desktop monitor-based group. Furthermore, we discuss the internal limiting factors of spatial cognition associated with head-mounted VRGIS and its potentials for supporting virtual geographic experiment development.