Objective It is intended to study the impact of normal young people's gender on their spatial navigation capabilities, and its relationship with the volume of the hippocampal subfields. Methods Sixty-three normal young volunteers were recruited to subject spatial navigation test and head magnetic resonance examination. The volume of the bilateral hippocampal subfields was obtained by FreeSurfer software. All subjects were divided into two groups by gender. Using partial correlation analysis to get the relationship between the spatial navigation ability and the hippocampal subfields' volume. Results The mixed spatial navigation ability of men in normal young healthy people was lower than that of women. The difference was found to be related to the smaller size of the right presubiculum and subiculum. Conclusion In healthy young people, there is a difference in the mixed spatial navigation ability between men and women, which due to the difference in the volume of the right presubiculum and subiculum. This study emphasizes the relationship between spatial navigation and hippocampus, lays a structural foundation for further understanding the spatial navigation processing capability.