Previous studies have demonstrated that alterations of gray matter exist in post-stroke aphasia (PSA) patients. However, so far, few studies combined structural alterations of gray matter volume (GMV) and intrinsic functional connectivity (iFC) imbalances of resting-state functional MRI to investigate the mechanism underlying PSA. The present study investigated specific regions with GMV abnormality in patients with PSA (n = 17) and age- and sex- matched healthy controls (HCs, n = 20) using voxel-based morphometry. In addition, we examined whether there is a link between abnormal gray matter and altered iFC. Furthermore, we explored the correlations between abnormal iFC and clinical scores in aphasic patients. We found significantly increased GMV in the right superior temporal gyrus, right inferior parietal lobule (IPL)/supramarginal gyrus (SMG), and left middle occipital gyrus. Decreased GMV was found in the right caudate gyrus, bilateral thalami in PSA patients. Patients showed increased remote interregional FC between the right IPL/SMG and right precuneus, right angular gyrus, right superior occipital gyrus; while reduced FC in the right caudate gyrus and supplementary motor area, dorsolateral superior frontal gyrus. Moreover, iFC strength between the left middle occipital gyrus and the left orbital middle frontal gyrus was positively correlated with the performance quotient. We suggest that GMV abnormality contributes to interregional FC in PSA. These results may provide useful information to understand the pathogenesis of post-stroke aphasia.