This study aimed to investigate the effects of electroacupuncture on cortical activation and swallowing muscle groups. The study examined brain activation in healthy subjects performing swallowing tasks during electroacupuncture. Additionally, the study analyzed electromyographic signals of swallowing muscle groups after electroacupuncture.Twenty-seven healthy subjects were randomly separated into three groups. They underwent electroacupuncture at HT5 acupoint (HT5 group), or GB20 acupoint (GB20 group), or HT5 + GB20 acupoint (HT5 + GB20 group) for 30 min of intervention. Subjects performed a swallowing task while receiving electroacupuncture. Functional near-infrared spectroscopy (fNIRS) was used to detect cortical activation and functional connectivity (FC). The mean amplitude values of the swallowing muscle groups after electroacupuncture were also measured. Statistical analysis was used to investigate the differences between the three groups. The protocol was registered with the China Clinical Trials Registry with the registration number ChiCTR2300067457.Compared with the HT5 group, the HT5 + GB20 group showed higher cortical activation in the LM1 (t = 2.842, P < 0.05) and a tighter FC in the RM1 and LM1 (t = 2.4629, P < 0.05) with considerably increased mean amplitude values of the swallowing muscle groups (t = 5.2474, P < 0.0001). Increased FC was found in the HT5 + GB20 group compared to the GB20 group between the RM1 and RS1 (t = 2.9997, P < 0.01), RM1 and RPM (t = 2.2116, P < 0.05), RM1 and LM1 (t = 3.2078, P < 0.01), RPM and LM1 (t = 2.7440, P < 0.05). However, there were no statistically significant differences in cortical activation or mean amplitude values of swallowing muscle groups.This study showed that electroacupuncture at HT5 + GB20 acupoints particularly engaged the cerebral cortex related to swallowing, resulting in tighter functional connectivity and higher amplitude values of swallowing muscle groups than electroacupuncture at single acupoints. The results may reveal the mechanism of electroacupuncture for post-stroke swallowing dysphagia.© 2023 The Authors.