Spatial ability is an influential factor for academic performance in Science, Technology, Engineering, and Mathematics (STEM) education. However, the roles of spatial strategies are unclear. Therefore, coupling with virtual Starmaze developed by fields of cognitive neuroscience, this study aimed to explore spatial strategy among STEM students and its role in academic performance. A virtual Starmaze was constructed to test how students complete a navigation test. A total of 172 college students majoring in STEM participated in this study. Modeling analysis showed students tend to use allocentric strategy when the difficulty of spatial tasks increased. Results further showed students with high STEM academic performance tended to use allocentric strategy while ones with low STEM academic performance tended to use egocentric strategy. Specifically, academic performances in science and mathematics learning were associated with the allocentric strategy, while academic performances in technology and engineering learning were associated with proficiency and hands-on ability.