Objective To observe the clinical effect of high frequency repetitive transcranial magnetic stimulation（ rTMS） on shoulder-hand syndrome after stroke. Methods A total of 60 patients with shoulder hand syndrome after stroke admitted to Department of Rehabilitation in Huaian Rehabilitation Hospital from June 2019 to October 2020 were divided into control group（ 30 cases） and treatment group（ 30 cases） by random number table method. Both groups received routine analgesic treatment and conventional rehabilitation treatment. On the basis of conventional treatment， the control group was given the pseudo rTMS treatment， and the treatment group was given 5 Hz rTMS treatment. The treatment was conducted 6 days a week for 2 weeks. During the treatment， 1 case fell off from the control group and 2 fell off from the treatment group. Visual analogue scale（ VAS） was used to evaluate the degree of pain. Fugl-Meyer Assessment-Upper Extremity（ FAM-UE） was used to evaluate the upper limb motor function. Drainage method was used to evaluate the swelling degree of affected forearm. Pittsburgh Sleep Quality Index（ PSQI） was used to evaluate the sleep state. Results After 2 weeks of treatment， the pain were relieved in both groups， and the difference was statistically significant（ P＜ 0.05）. The pain improvement degree of the treatment group was better than that of the control group， and the difference was statistically significant［ VAS=（4.85±0.86） in the control group and（ 4.30±1.10） in the treatment group， P ＜ 0.05］. The motor function of affected limb was improved in both groups after treatment， and the differences were statistically significant（ P＜0.05）. The improvement degree of the treatment group was better than that of the control group［ FMA-UE=（31.00±4.00） in the control group， FMA-UE=（35.89±4.74） in the treatment group， P ＜ 0.05］. The degree of swelling of affected limbs in the two groups was significantly lower than that before treatment， and the differences were statistically significant（ P ＜ 0.05）. The degree of swelling reduction in the treatment group was better than that in the control group［ （52.85±12.48） ml in the control group，（ 47.70±11.17） ml in the treatment group， P＜0.05］. The sleep quality of the two groups was significantly improved after treatment， and the differences were statistically significant（ P ＜ 0.05）. There was no statistical significance in the difference of sleep quality between the two groups［ PSQI=（7.70±2.00） in the control group and（ 7.37±2.26） in the control group， P＞ 0.05］. Conclusions High frequency rTMS can significantly improve the degree of pain and clinical symptoms in patients with shoulder-hand syndrome after stroke， however two weeks of high frequency rTMS treatment can not significantly improve sleep quality compared with conventional treatment.