Background Electroacupuncture (EA) has been shown to facilitate brain plasticity‐related functional recovery following ischemic stroke. The functional magnetic resonance imaging technique can be used to determine the range and mode of brain activation. After stroke, EA has been shown to alter brain connectivity, whereas EA's effect on brain network topology properties remains unclear. An evaluation of EA's effects on global and nodal topological properties in rats with ischemia reperfusion was conducted in this study. Methods and results There were three groups of adult male Sprague‐Dawley rats: sham‐operated group (sham group), middle cerebral artery occlusion/reperfusion (MCAO/R) group, and MCAO/R plus EA (MCAO/R + EA) group. The differences in global and nodal topological properties, including shortest path length, global efficiency, local efficiency, small‐worldness index, betweenness centrality (BC), and degree centrality (DC) were estimated. Graphical network analyses revealed that, as compared with the sham group, the MCAO/R group demonstrated a decrease in BC value in the right ventral hippocampus and increased BC in the right substantia nigra, accompanied by increased DC in the left nucleus accumbens shell (AcbSh). The BC was increased in the right hippocampus ventral and decreased in the right substantia nigra after EA intervention, and MCAO/R + EA resulted in a decreased DC in left AcbSh compared to MCAO/R. Conclusion The results of this study provide a potential basis for EA to promote cognitive and motor function recovery after ischemic stroke. Graph theory studies of functional networks show significant changes in the brain regions associated with the process of cognitive and motor functions after ischemic stroke. Electroacupuncture at LI11 and ST36 acupoints could affect the network topological measures in cognitive and motor‐related brain areas, and these changes are related to acupoint specificity.