Ischemic stroke (IS) is associated with high morbidity, mortality, and disability rates. The pathological mechanism of motor dysfunction in stroke need to be determined to improve the effectiveness of rehabilitation therapy. Clinical data, electroencephalography (EEG) data, and functional magnetic resonance imaging (fMRI) data were collected from 86 patients with IS and 45 healthy controls. The EEG signals were analyzed via wavelet transform, brain network construction. The fMRI results were analyzed based on brain network construction. Low-frequency energy activity was found in stroke patients; Neural adaptation slowed, and the number and intensity of brain network functional connectivity (FC) in patients were significantly reduced. The results of the fMRI examination revealed that the strength of the brain network correlation matrix was significantly weaker, and the brain network graph theory properties decreased considerably. The decrease in brain network connectivity and the overall decline in the brain network graph theory attribute index may be the key mechanisms underlying the occurrence of lower limb motor dysfunction.