Objective: To explore the changes in gray matter volume of the cerebral cortex in patients with intermittent exotropia (IXT) using the voxel-based analysis and to analyze the correlation between these changes and clinical manifestations. Methods: This was a cross-sectional study. A collection of 15 consecutive patients diagnosed with IXT at Tianjin Eye Hospital from March 2021 to May 2022 formed the exotropia group, which comprised 8 males and 7 females, with an average age of (23.5±5.2) years. Ten healthy individuals, 3 males and 7 females, with an average age of (27.0±7.5) years, were selected as the control group. All participants underwent assessments of exotropia severity and Titmus stereoacuity. Three-dimensional high-resolution brain images were obtained through MRI scans. Voxel-based morphometry was employed to preprocess the MRI data, and the SPM toolbox in MATLAB was utilized to analyze differences of images between the two groups. Regions of interest (ROI) with structural abnormalities in the gray matter volume analysis were selected, and the ratio of gray matter voxel values in the ROI to the mean gray matter voxel values of the whole brain for each participant was calculated using the MarsBaR software. The correlation between this ratio and exotropia severity as well as the common logarithm of Titmus stereoacuity was analyzed. Results: The differences in age, gender distribution, and refractive error between the two groups were not statistically significant (all P>0.05). However, there were statistically significant differences in the degree of strabismus and Titmus stereoacuity (both P<0.001). Compared to the control group, patients in the strabismus group exhibited decreased gray matter volume in several brain regions, including the wedges of the medial surface of the cerebral hemisphere (decreased by 89 voxels), the left lingual gyrus (decreased by 176 voxels), the left calcarine sulcus V3 area (decreased by 30 voxels), the central anterior gyrus of the right frontal lobe (decreased by 192 voxels), the gray matter of the left hippocampal gyrus (decreased by 20 voxels), and the bilateral lateral geniculate nuclei (decreased by 100 and 40 voxels on the left and right sides, respectively). These differences were all statistically significant (all P<0.001). Additionally, there was an increase in gray matter volume in several brain regions, including the bilateral caudate nuclei (increased by 60 and 76 voxels on the left and right sides, respectively) and the left precentral gyrus (increased by 36 voxels). These differences were also statistically significant (all P<0.001). A group-level analysis identified 10 brain regions with structural differences between the two groups, which were used as ROI. The gray matter volume ratio was negatively correlated with the degree of exotropia (all P<0.05) in the ROI of the left wedges (r=-0.670), left calcarine sulcus V3 area (r=-0.610), and left lingual gyrus (r=-0.684). The gray matter volume ratio was negatively correlated with lgTS (all P<0.05) in the ROI of the left wedges (r=-0.568) and the central anterior gyrus of the right frontal lobe (r=-0.563). Conclusions: Patients with IXT exhibit decreased gray matter volume in the horizontal connection areas between the primary visual cortices V1 and V2. The reduction in gray matter volume of the lingual gyrus and the dorsal visual pathway V3 area becomes more pronounced with increasing exotropia severity, while the gray matter volume of the precentral gyrus (BA6 area) decreases with worsening stereoacuity.