To explore the effect of transcranial magnetic stimulation combined with Tongdu Liqiao acupuncture on the risk of aspiration pneumonia in patients with dysphagia after cerebral infarction, and to analyze the changes in swallowing function based on the Difference-in-Differences (DID) model. Methods: A total of 120 patients diagnosed with dysphagia after cerebral infarction admitted to our hospital from October 2022 to April 2024 were divided into an acupuncture group and a combined group via the random number table method, with 60 patients in each group. Both groups received Tongdu Liqiao acupuncture, and the combined group was additionally treated with transcranial magnetic stimulation. The clinical efficacy and incidence of aspiration pneumonia were compared between the two groups. The DID model was used to compare the changes in swallowing function before and after treatment. Patients were further subdivided into a pneumonia subgroup and a non-pneumonia subgroup according to whether aspiration pneumonia occurred. Multivariate Cox regression analysis was conducted to analyze the influencing factors for aspiration pneumonia in patients with post-cerebral infarction dysphagia. Results: After 1 month of treatment, the total effective rate in the combined group was higher than that in the acupuncture group (P<0.05). At 2 weeks and 4 weeks after treatment, the SSA scores of the combined group were lower, while the FOIS scores were higher compared with the acupuncture group (P<0.05). DID regression results revealed more prominent changes in SSA and FOIS scores in the combined group relative to the acupuncture group. The treatment effect interacted with time; with prolonged treatment duration, the SSA score decreased by 76.38% and the FOIS score increased by 30.92% (P<0.05). There was a statistically significant difference in the incidence of aspiration pneumonia between the two groups, and the incidence curve of aspiration pneumonia in the combined group was lower than that in the acupuncture group (P<0.05). Conclusion: Transcranial magnetic stimulation combined with Tongdu Liqiao acupuncture can improve the overall therapeutic efficacy, accelerate the recovery of swallowing function, and prevent the occurrence of aspiration pneumonia in patients with dysphagia after cerebral infarction.