Objective To investigate electroacupuncture (EA)-induced reorganization of voxel-mirrored homotopic connectivity (VMHC) and its association with motor recovery in a rat model of ischemic stroke.Methods Twenty-four female Sprague-Dawley rats were randomized into Sham group, stroke model group and EA group. The EA group received 1-week treatment (2/15 Hz sparse-dense wave, 2 mA, 30 min/day) at GV20. Neurological deficits were assessed using the modified neurological severity score. And resting-state functional magnetic resonance imaging was acquired pre-post-intervention for VMHC analysis. Group differences and VMHC-behavior correlations were evaluated.Results EA significantly increased VMHC in subcortical motor regions (p = 0.001, alphasim correction) but decreased VMHC in somatosensory cortex versus untreated stroke. Model group showed progressive VMHC reductions in hippocampus, hypothalamus, and somatosensory cortex. Enhanced internal capsule VMHC correlated with improved Longa scores in EA rats (r2 = 0.206, p = 0.009).Conclusion EA promotes motor recovery through frequency-specific bidirectional VMHC modulation. This study elucidates EA's inter-hemispheric connectivity level therapeutic mechanism for stroke rehabilitation.