A number of studies have suggested that motor imagery training (MIT) has a positive influence on the upper extremity motor recovery in stroke patients, but little is known about its neural basis. To investigate the cortical motor network plasticity after MIT, 34 chronic hemiplegic subjects with subcortical stroke were recruited and randomly allocated to either the conventional rehabilitation therapy (CRT) or the CRT + MIT. The patients were assessed with the upper limb section of Fugl-Meyer assessment Scale (FM-UL) and resting-state fMRI before and after the 4 weeks of treatment. Seed-based functional connectivity (FC) of the ipsilesional primary motor cortex (M1) and graph-theory based analysis were used to explore the relationships between the motor recovery and reorganization of motor networks. We found that the patients in the MIT group showed more improvement in the FM-UL scores compared with the CRT group. Both groups presented increased inter-hemispheric and decreased intra-hemispheric FC of the ipsilesional M1 after intervention. However, the MIT group showed increased FC of the ipsilesional M1 with the ipsilesional precentral and postcentral gyri, middle cingulate gyrus and supramarginal gyrus after intervention, while the CRT group showed decreased FC in these regions. In addition, the clustering coefficient was significantly increased in the MIT group but not in the CRT group, and the increment of clustering coefficient was significantly positively correlated with improvement of FM-UL scores. Therefore, MIT might contribute to the motor recovery in stroke patients through the following network reorganization, i.e., promoting the efficiency of regional neuronal communication and the reorganization of intrinsic FC of the ipsilesional M1 involving widely distributed motor network in both hemispheres.