This study investigated local and global changes in the motor network using longitudinal resting-state functional magnetic resonance imaging (rs-fMRI). Motor impairment was measured in 81 stroke patients using Fugl-Meyer assessment on the same day as rs-fMRI acquisition at both 2 weeks and 3 months post-stroke. The relationships between network measures and motor function scores were assessed. With regard to local connectivity, interhemispheric connectivity was noticeably altered at each time point. Interhemispheric connectivity was also related to residual motor function and improvement in motor function. The anterior intraparietal sulcus and other well-known primary and secondary motor-related regions played important roles in motor function. Changes in global connectivity according to stroke type and initial severity were investigated. In global connectivity, interhemispheric connectivity was disrupted at 2 weeks post-stroke regardless of stroke type and initial severity. During the recovery period, interhemispheric connectivity recovered well in patients with hemorrhagic stroke or low severity. In contrast, there were no significant between-group and within-group alterations in intrahemispheric connectivity. Intrahemispheric connectivity of the inferior frontal cortex (IFC) exhibited opposite alterations compared to other connections. There were no differences between groups in IFC connectivity alterations; however, decreasing ipsilesional IFC connectivity and contralesional IFC during recovery were noticeable in patients with mild to moderate impairments and patients with severe impairments, respectively. These results may be helpful in understanding the network changes that occur after stroke and could have important implications for treatment strategy development in future studies.