Objective To investigate the differences in the topology of functional brain networks between populations with good spatial navigation ability and those with poor spatial navigation ability. Methods From September 2020 to September 2021, 100 college students from PLA Army Border and Coastal Defense Academy were selected to test the spatial navigation ability. The 25 students with the highest spatial navigation ability were selected as the GN group, and the 25 with the lowest spatial navigation ability were selected as the PN group, and their resting-state functional MRI and 3D T1-weighted structural image data of the brain were collected. Graph theory analysis was applied to study the topology of the brain network, including global and local topological properties. Results The variations in the clustering coefficient, characteristic path length, and local efficiency between the GN and PN groups were not statistically significant within the threshold range (P>0.05). The brain functional connectivity networks of the GN and PN groups met the standardized clustering coefficient (γ)>1, the standardized characteristic path length (λ)≈1, and the small-world property (σ)>1, being consistent with small-world network property. The areas under curve (AUCs) for global efficiency (0.22±0.01 vs. 0.21±0.01), γ value (0.97±0.18 vs. 0.81±0.18) and σ value (0.75±0.13 vs. 0.64±0.13) of the GN group were higher than those of the PN group, and the differences were statistically significant (P<0.05); the between-group difference in AUC for λ value was not statistically significant (P>0.05). The results of the nodal level analysis showed that the AUCs for nodal clustering coefficients in the left superior frontal gyrus of orbital region (0.29±0.05 vs. 0.23±0.07), the right rectus gyrus (0.29±0.05 vs. 0.23±0.09), the middle left cingulate gyrus and its lateral surround (0.22±0.02 vs. 0.25±0.02), the left inferior occipital gyrus (0.32±0.05 vs. 0.35±0.05), the right cerebellar area 3 (0.24±0.04 vs. 0.26±0.03), and the right cerebellar area 9 (0.22±0.09 vs. 0.13±0.13) were statistically different between the two groups (P<0.05). The differences in AUCs for degree centrality and nodal efficiency between the two groups were not statistically significant (P>0.05). Conclusions Compared with people with good spatial navigation ability, the topological properties of the brains of the ones with poor spatial navigation ability still conformed to the small-world network properties, but the connectivity between brain regions reduces compared with the good spatial navigation ability group, with a tendency to convert to random networks and a reduced or increased nodal clustering coefficient in some brain regions. Differences in functional brain network connectivity exist among people with different spatial navigation abilities.