Intervention with combined low-frequency repetitive transcranial magnetic stimulation and intensive occupational therapy can improve brain function in poststroke patients with motor paralysis. We aimed to evaluate the relationship between brain structure at the time of intervention and the degree of motor function improvement using this combination therapy. Twenty-five patients with upper limb paralysis after stroke were hospitalized for 15 days to receive 12 sessions of low-frequency repetitive transcranial magnetic stimulation over the nonlesional hemisphere and occupational therapy. Imaging analysis was carried out using three-dimensional T1-weighted images. Correlation analysis between cortical thickness and upper limb motor function score was carried out using FreeSurfer. Correlation analysis between cortical thickness and motor function improvement was carried out by atlas-based analysis. FreeSurfer showed that significant positive correlations were found between cortical thickness of the postcentral or supramarginal gyrus of the diseased hemisphere and motor function improvements in nondominant hand paralysis (uncorrected P<0.001). Results using the atlas supported these results (P<0.05). The results of the analysis indicated that the effect of our proposed treatment could be related to the cortical thickness. In particular, it is considered that the cortical thickness of the postcentral gyrus or the supramarginal gyrus of the affected hemisphere plays an important role in such recovery in poststroke hemiparetic patients.