The relationship between structural changes in the cerebral gray matter and diminished balance control performance in patients with chronic ankle instability (CAI) has remained unclear. This paper aimed to assess the difference in gray matter volume (GMV) between participants with CAI and healthy controls (HC) and to characterize the role of GMV in the relationship between disease duration and balance performance in CAI. 42 participants with CAI and 33 HC completed the structural brain MRI scans, one‐legged standing test, and Y‐balance test. Regional GMV was measured by applying voxel‐based morphometry methods. The result showed that, compared with HC, participants with CAI exhibited lower GMV in multiple brain regions (familywise error [FWE] corrected p < 0.021). Within CAI only, but not in HC, lower GMV in the thalamus (β = −0.53, p = 0.003) and hippocampus (β = −0.57, p = 0.001) was associated with faster sway velocity of the center of pressure (CoP) in eyes closed condition (i.e., worse balance control performance). The GMV in the thalamus (percentage mediated [PM] = 32.02%; indirect effect β = 0.119, 95% CI = 0.003 to 0.282) and hippocampus (PM = 33.71%; indirect effect β = 0.122, 95% CI = 0.005 to 0.278) significantly mediated the association between the disease duration and balance performance. These findings suggest that the structural characteristics of the supraspinal elements is critical to the maintenance of balance control performance in individuals suffering from CAI, which deserve careful consideration in the management and rehabilitation programs in this population.