Background: Stroke survivors are known to suffer from post-stroke depression (PSD). However, the likelihood of structural changes in the brains of PSD patients has not been explored. This study aims to extract changes in the gray matter of these patients and test how these changes account for the PSD symptoms. Methods: High-resolution T1 weighted images were collected from 23 PSD patients diagnosed with subcortical stroke. Voxel-based morphometry and support vector machine analyses were used to analyze the data. The results were compared with those collected from 33 non-PSD patients. Findings: PSD group showed decreased gray matter volume (GMV) in the left middle frontal gyrus (MFG), and increased GMV in the right anterior cingulate gyrus (ACG) when compared to the non-PSD patients. The changes in GMVs in the MFG and ACG suggest possible systemic involvement of the prefrontal-limbic network resulting in PSD after brain lesions which is likely to be independent from the location of the lesions. Furthermore, the combined GMV values of the MFG and ACG distinguished 81% of the PSD from the non-PSD patients (76·5% sensitivity and 87·5% specificity). Interpretation: The MFG-ACG model suggests that the PSD diagnosis is likely to attribute to abnomrmality in the prefrontal-limbic network. Reduced emotional control resulting in hyperactive emotional processing seems to aggravate the PSD symptoms of the post-stroke patients. Funding: This study was supported by the Department of Rehabilitation Medicine, Nanjing Drum Tower Hospital and the University Research Facility of Behavioral and Systems Neuroscience (UBSN), The Hong Kong Polytechnic University. Declaration of Interest: The authors declare no potential conflicts of interest. Ethical Approval: The research protocol and implementation were in accordance with the Declaration of Helsinki. Written informed consent was obtained from each patient and the ethics approval was obtained from the research committee of the hospital in which the study was conducted.