To simultaneously perform dual stimulation (DS) through repetitive transcranial magnetic stimulation (rTMS) and resistance training of the target muscle group (submental muscles) using chin-tuck against resistance (CTAR), with the aim of observing via functional near-infrared spectroscopy (fNIRS) and surface electromyography studies whether rTMS and CTAR dual stimulation can maximize cerebral blood oxygenation and brain connectivity changes, as well as submental muscle contraction function, thus enhancing swallowing function and providing a new treatment method to reduce clinical swallowing disorder patients' risk of aspiration. Forty age-matched healthy participants were enrolled and assigned to four groups: the first group received no intervention, the second group received 5-Hz single stimulation via rTMS on the dominant hemisphere M1; the third group received simultaneous 5-Hz rTMS on the dominant hemisphere M1 with active resistance movement DS of the submental muscles; the last group received single stimulation via CTAR; all participants were assessed before and after stimulation through fNIRS to measure cerebral hemodynamics for evaluating differences in brain area activation and functional connectivity during resting and task states. Differences in the root mean square amplitude (RMS) of the submental muscle group among the four groups were also analyzed. DS group channels 24 and 51 showed higher cortical activation; also increased connectivity from the left frontal lobe to the right parietal lobe. In bilateral submental muscle groups, RMS after intervention was significantly reduced in DS group and CTAR group, while there was no significant difference between TMS group and control group. In conclusion, dual stimulation of rTMS combined with CTAR can significantly activate the cerebral cortex, increase brain connectivity and reduce RMS in the rehabilitation of dysphagia, which is a promising treatment method and provides a basis for non-invasive research of fNIRS.