Objective To explore the clinical therapeutic value of repetitive transcranial magnetic stimulation with intermittent Theta burst stimulation （iTBS） combined with neuromuscular electrical stimulation （NMES） in post-stroke dysphagia （PSD）. Methods From November 2022 to October 2023， 60 PSD patients admitted to the rehabilitation department of Xuzhou Central Hospital were selected as research subjects. Patients were randomly divided into NMES group and NMES + iTBS group using a random number table method， with 30 cases in each group. Both groups of patients were treated with routine swallowing rehabilitation training. NMES group received NMES on this basis， while NMES + iTBS group received repetitive transcranial magnetic stimulation with iTBS in the cortical representative area of the superior hyoid muscle group on the healthy side of the patient's brain on the basis of NMES group. Both groups carried out continuous treatment for two weeks. Before and after treatment， swallowing disorder imaging was performed on the patient， and the Videofluoroscopic Dysphagia Scale （VDS） score and Rosenbek Penetration-Aspiration Scale （PAS） grading were evaluated based on the examination results. The swallowing function was assessed using the Standardized Swallowing Assessment Scale （SSA） and Water Swallow Test （WST） grading. Results Before treatment， there was no statistically significant difference in VDS score， PAS grading， SSA score， and WST grading between the two groups of patients （Z=-0.371、-0.718、-0.507、-1.104；all P＞ 0.05）. After treatment， the VDS score， PAS grading， SSA score， and WST grading of the two groups of patients were lower than before treatment， and the score and grading of patients in the NMES + iTBS group were better than those in NMES group， and the differences were statistically significant （Z=-5.412 - -3.884；all P ＜ 0.05）. Conclusions The combination of repetitive transcranial magnetic stimulation with iTBS and NMES can effectively promote the recovery of swallowing function in PSD patients.