We evaluated the association between cardiorespiratory fitness (CRF) and executive function (EF) in young adults and the mediating effects of GMV on this relationship. This study involved 217 college students. An incremental load exercise program was used to evaluate VO₂max. EF was estimated by the Flanker task, the 2-back task, and the more-odd shifting task, while structural magnetic resonance and region-based morphometry (RBM) were used to analyze GMV. The high CRF group had a shorter updating reaction time (RT) (p ≤ 0.05). CRF was positively correlated with the right orbital part of the middle frontal gyrus (ORBmid.R) GMV (p ≤ 0.05). ORBmid.R GMV was negatively correlated with updating RT (p ≤ 0.05). Model 4 in SPSS was used to assess the mediating effects of ORBmid.R GMV between CRF and updating RT. ORBmid.R GMV was established to have a partially mediating role between CRF and updating RT, which accounted for 19.6% of the total effect value. These findings indicate that the negative correlation between CRF and EF was significant, and ORBmid.R GMV played a mediating role in the relationship between CRF and EF, providing new evidence toward comprehensively revealing that CRF promotes EF performance.