Objective To analyze the changes in structure of whole brain gray matter in patients with type 2 diabetes mellitus (T2DM) and cognitive impairment (CI) by voxelbased brain morphological MRI method. Methods 40 cases of patients with T2DM complicated with CI (D-CI group) and 45 patients with T2DM and without CI (T2DM group) treated in our hospital from February 2011 to January 2016 were enrolled in the study. Another 30 healthy subjects were selected as the control group at the same time. After admission, patients in the three groups were examined with conventional MRI and three-dimensional magnetization prepared rapid gradient echo to collect the whole brain volume data, and the data were processed by using VBM8 tools. The gray matter and white matter volume was statistically analyzed, and its relationship with CI was analyzed by the partial correlation analysis. Results There was no significant difference among the three groups in the total volume of cerebral white matter (P>0.05). The total gray matter volume showed D-CI group < T2DM group < the control group (P<0.05). There was no significant difference among groups in gray matter volume, white matter volume and brain volume (TIV) (P>0.05). The left and right cerebral hippocampal volume showed D-CI group < T2DM group < the control group, and the gray matter structure volume in the other zones showed no statistically significant difference (P>0.05). The left middle temporal gyrus volume, left cerebral hippocampal volume and right cerebral hippocampal volume of patients with T2DM were negatively correlated with the degree of cognitive impairment (r=-0.697, -0.415, -0.512, P<0.05). Conclusion Patients with T2DM and patients with T2DM complicated with CI have gray matter volume atrophy in different areas of the brain, and brain atrophy is more severe in patients with T2DM complicated with CI. The decrease of gray matter volume in the middle temporal gyrus and the hippocampus is more obvious.