This study aimed to investigate the changes in functional connectivity (FC) within each resting-state network (RSN) and between RSNs in subcortical stroke patients who were well recovered in global motor function. Eleven meaningful RSNs were identified via functional magnetic resonance imaging data from 25 subcortical stroke patients and 22 normal controls using independent component analysis. Compared with normal controls, stroke patients exhibited increased intranetwork FC in the sensorimotor (SMN), visual (VN), auditory (AN), dorsal attention (DAN), and default mode (DMN) networks; they also exhibited decreased intranetwork FC in the frontoparietal network (FPN) and anterior DMN. Stroke patients displayed a shift from no FC in controls to negative internetwork FC between the VN and AN as well as between the VN and SMN. Stroke patients also exhibited weakened positive (anterior and posterior DMN; posterior DMN and right FPN) or negative (AN and right FPN; posterior DMN and dorsal SMN) internetwork FC when compared with normal controls. We suggest that subcortical stroke may induce connectivity changes in multiple functional networks, affecting not only the intranetwork FC within RSNs but also the internetwork FC between these RSNs.