【Abstract】 Objective To investigate the effects of repetitive transcranial magnetic stimulation (rTMS) on motor function recovery after ischemic stroke by using amplitude of low frequency fluctuation (ALFF) and clinical assessments.Methods 15 patients were assigned to rTMS treatment (RT) group (8 cases) and conventional treatment (CT) group (7 cases). The patients in RT group received 10 Hz rTMS treatment for 10 days plus conventional treatment. The FuglMeyer (FM), Barthel Index (BI) and ALFF were measured before and after treatment in the two groups.Results The FM and BI scores significantly increased after treatment in rTMS group and CT group (P＜0.05). FM and BI scores had significantly difference between rTMS group and CT group (P＜0.05). In addition, there was a significant difference in ALFF between the two groups after treatment (P＜0.05). The ALFF significantly increased in the right putamen and left cerebellum, and ALFF significantly decreased in the bilateral primary motor cortex (M1), bilateral SMA, right thalamic and right cerebellum.Conclusion HFrTMS may improve the motor dysfunction after ischemic stroke. This might be associated with the mechanism that rTMS affects the neuronal activity of movementrelated areas in the brain.