To provide a research basis for optimizing rehabilitation scheme for post-stroke hemiplegia by observing altered function connectivity of the basal ganglia in patients with post-stroke hemiplegia using resting state fMRI. Methods:We recruited 21 patients with left hemiplegia and 20 healthy subjects with the age, gender and degree of culture matched. We scanned all subjects in the resting state via magnetic resonance imaging and compared the differences of the functional connectivity（FC）between the seed points（7 pairs of Subcortical nuclei）and whole brain regions of the patients and healthy subjects. Results:Compared with healthy subjects, the decrease of functional connection was mainly located on the left caudate and the right medial frontal gyrus, temporal lobe, cerebellar posterior and caudal nucleus, and the left frontal gyrus, parietal lobe and temporal lobe; The right caudate nucleus and the left frontal gyrus, frontal lobe, cingulate gyrus, cerebellum posterior lobe, thalamus, and the right frontal gyrus; the left putamen and the right cingulate and thalamus; the right putamen and the left cingulate and thalamus; the left thalamus and right frontal lobe, temporal lobe and cingulate gyrus; the right thalamus and the left Parahippocampal gyrus and cingulate, right parietal lobe and precuneus. Functional connection enhancement could be seen mainly in the right caudate and right parietal lobe; right accumbens and right globus; the right globus and the right parietal lobe and putamen; the left globus and the left middle occipital gyrus. Conclusion:The decrease and enhancement in bilateral hemisphere coexisted in patients with hemiplegia who are in the left side of the recovery period. The functional connectivity between the cortex and basal ganglia decreased between bilateral cerebral hemisphere and increased within unilateral cerebral hemisphere.