Brain-computer interface (BCI) based rehabilitation has been proven a promising method facilitating motor recovery. Recognizing motor intention is crucial for realizing BCI rehabilitation training. Event-related desynchronization (ERD) is a kind of electroencephalogram (EEG) inherent characteristics associated with motor intention. However, due to brain deficits poststroke, some patients are not able to generate ERD, which discourages them to be involved in BCI rehabilitation training. To boost ERD during motor imagery (MI), this paper investigates the effects of high-frequency repetitive transcranial magnetic stimulation (rTMS) on BCI classification performance. Eleven subjects participated in this study. The experiment consisted of two conditions: rTMS + MI versus sham rTMS + MI, which were arranged on different days. MI tests with 64-channel EEG recording were arranged immediately before and after rTMS and sham rTMS. Time-frequency analysis were utilized to measure ERD changes. Common spatial pattern was used to extract features and linear discriminant analysis was used to calculate offline classification accuracies. Paired-sample t-test and Wilcoxon signed rank tests with post-hoc analysis were used to compare performance before and after stimulation. Statistically stronger ERD (-13.93±12.99%) was found after real rTMS compared with ERD (-5.71±21.25%) before real rTMS (p<0.05). Classification accuracy after real rTMS (70.71±10.32%) tended to be higher than that before real rTMS (66.50±8.48%) (p<0.1). However, no statistical differences were found after sham stimulation. This research provides an effective method in improving BCI performance by utilizing neural modulation.Clinical Relevance- This study offers a promising treatment for patients who cannot be recruited in BCI rehabilitation training due to poor BCI classification performance.