BACKGROUND The combined effects of bilateral corticospinal tract (CST) reorganization and interhemispheric functional connectivity (FC) reorganization on motor recovery of upper and lower limbs after stroke remain unknown. MATERIAL AND METHODS A total of 34 patients underwent magnetic resonance imaging (MRI) examination at weeks 1, 4, and 12 after stroke, with a control group of 34 healthy subjects receiving 1 MRI examination. Interhemispheric FC in the somatomotor network (SMN) was calculated using the resting-state functional MRI (rs-fMRI). Fractional anisotropy (FA) of bilateral CST was recorded as a measure of reorganization obtained from diffusion tensor imaging (DTI). After intergroup comparisons, multiple linear regression analysis was used to explore the effects of altered FA and interhemispheric FC on motor recovery. RESULTS Interhemispheric FC restoration mostly occurred within 4 weeks after stroke, and FA in ipsilesional remained CST consistently elevated within 12 weeks. Multivariate linear regression analysis showed that the increase in both interhemispheric FC and ipsilesional CST-FA were significantly correlated with greater motor recovery from week 1 to week 4 following stroke. Moreover, only increased FA of ipsilesional CST was significantly correlated with greater motor recovery during weeks 4 to 12 after stroke compared to interhemispheric FC. CONCLUSIONS Our results show dynamic structural and functional reorganizations following motor stroke, and structure reorganization may be more related to motor recovery at the late subacute phase. These results may play a role in guiding neurological rehabilitation.