Objective To investigate the therapeutic effect of repeated transcranial magnetic stimulation （rTMS） combined with hydrogel feeding training on patients with dysphagia following subacute cerebral infarction， as well as its impact on swallowing function. Methods From February 2022 to February 2024， 102 patients with dysphagia after subacute cerebral infarction treated in our hospital were selected and divided into control group， sham stimulation group and observation group， with 34 cases in each group. The control group received hydrogel feeding training， the sham stimulation group received sham stimulation on the basis of the control group， and the observation group received repeated transcranial magnetic stimulation on the basis of the control group. The swallowing function， quality of life， nerve function， neurotrophic factor， nutritional status， respiratory function， cerebral blood flow signal and clinical efficacy of the two groups were measured and compared. Results Compared with pre-treatment， the leak-aspiration score scale （PAS）， NIHSS score， and pulse index （PI） were significantly reduced in all groups after treatment. Moreover， the observation group exhibited lower values than both the control group and the pseudostimulation group （P < 0.05）. In contrast， functional oral intake scale （FOIS）， dysphagia-specific quality of life （SWAL-QOL） score， brain-derived neurotrophic factor （BDNF）， nerve growth factor （NGF）， insulin-like growth factor 1 （IGF-1）， hemoglobin （Hb）， albumin （ALB）， forced vital capacity （FVC）， one-second forced expiratory volume （FEV1）， peak expiratory flow （PEF）， peak systolic velocity （PSV）， end-diastolic velocity （EDV）， and mean velocity （MV） were significantly increased after treatment compared to pre-treatment. The observation group demonstrated higher values for these parameters compared to the control group and pseudostimulation group （P < 0.05）. Additionally， the clinical efficacy in the observation group was significantly higher （P < 0.05）. Conclusion The combination of repeated transcranial magnetic stimulation and hydrogel feeding training for patients with dysphagia following subacute cerebral infarction can effectively enhance swallowing function， mitigate nerve damage， and improve both nutritional status and quality of life.