In morphometric neuroimaging studies, the relationship between brain structural changes and the antidepressant treatment response in patients with major depressive disorder has been explored to search depression-trait biomarkers. Although patients were treated with serotonin-related drugs, whether the same treatment resulted in remission and non-remission in depressed patients is currently under investigation. We recruited 25 depressed patients and 25 healthy controls and acquired volumetric magnetic resonance imaging of each participant. We used the shape index and curvedness to classify cortical shapes and quantify shape complexities, respectively, in studying the pharmacological effect on brain morphology. The results showed that different regions of structural abnormalities emerged between remitting and non-remitting patients when contrasted with healthy controls. In addition to comparing structural metrics in each cortical parcellation, similar to the traditional voxel-based morphometric method, we highlighted the importance of structural integrity along the serotonin pathway in response to medication treatment. We discovered that disrupted serotonin-related cortical regions might cause non-remission to antidepressant treatment from a pharmacological perspective. The anomalous areas manifested in non-remitting patients were mainly in the frontolimbic areas, which can be used to differentiate remitting from non-remitting participants before medication treatment. Because non-remission is the failure to respond to treatment with serotonin-related drugs, our method may help clinicians choose appropriate medications for non-remitting patients.