Objective Combined with resting-state functional magnetic resonance imaging (rs-fMRI) to explore the effect of repetitive transcranial magnetic stimulation (rTMS) on mild cognitive impairment（MCI）and its effect on local neural activity.Methods A total of 29 MCI subjects who met the diagnostic criteria in Nanchong were included and divided into two groups， including 12 Sham group and 17 rTMS group. rTMS group was treated with high frequency rTMS for 10 days in the right Dorsolateral Prefrontal Cortex (DLPFC).The stimulus parameters of Sham group were identical to those of rTMS group， but the coil could not produce real and effective stimulus. Subjects in both groups underwent mini-Mental State Examination (MMSE)， Montreal Cognitive Scale (MoCA) and rs-fMRI data acquisition 1 day before and on the day after treatment. The changes and differences of MMSE， MoCA score and regional homogeneity (Reho) within and between the two groups before and after treatment were compared and analyzed. The correlation between the changes of Reho and the changes of MMSE and MoCA scores in different brain regions was further analyzed.Results The scores of MMSE and MoCA in rTMS group were significantly higher than before treatment(P<0.05)， the MoCA scale score of Sham group was higher after treatment than before treatment (P<0.05)， and there was no significant difference in MMSE scale score compared with before treatment (P>0.05). The change of MMSE scale score in rTMS group was better than that in Sham group before and after treatment (P=0.048). Compared with before treatment， ReHo value increased in the left parietal lobe， anterior and posterior central gyrus， inferior frontal gyrus， right precuneus， angular gyrus， bilateral middle cingulate gyrus， posterior cingulate gyrus， occipital lobe and cerebellum in the rTMS group after treatment. The regions with decreased ReHo included: left superior marginal gyrus， right auxiliary motor cortex， middle frontal gyrus， superior frontal gyrus， superior temporal gyrus， central sulcus tegmental area. In the rTMS group， the change of ReHo value in the left inferior frontal gyrus before and after treatment was significantly positively correlated with the change of MMSE scale score (R=0.662， P=0.005).Conclusion High-frequency rTMS stimulation over the right DLPFC in patients with MCI can improve the cognitive function of patients and improve the local neural activity in related brain regions.