The relationship between motor recovery and changes in brain structural and functional connectivity after stroke remains unclear. This study quantified the correlation between post-stroke white matter changes and functional responses and explored the brain network mechanism of contralesional primary motor cortex (cM1) low-frequency repetitive transcranial magnetic stimulation (LF-rTMS) affecting the motor recovery after stroke. Fifty patients accepted cM1 LF-rTMS or sham stimulation. The changes in structural-functional (SC-FC) coupling at the whole-brain, hemispheric, and modular levels were evaluated. Hemispheric SC-FC coupling lateralization index (LI), intramodular and intermodular connectivity, and node participant coefficient (PC) were further analyzed. The motor function score of the rTMS group improved more significantly, which was positively correlated with the whole brain and the affected-side somatosensory/motor and auditory network SC-FC coupling, the hemispheric SC-FC coupling LI, the intermodular connectivity between the intact-side default mode network and the affected-side limbic/paralimbic and subcortical network, but negatively correlated with the SC-FC coupling in the intact-side hemisphere and somatosensory/motor and auditory network. cM1 LF-rTMS can regulate structural changes and functional responses of the whole-brain, hemispheric, and modular levels after stroke, and effectively promote the improvement of upper limb motor function. SC-FC coupling may be a sensitive biomarker for predicting post-stroke motor recovery.