Objective To investigate the change in the activation of brain functional areas during swallowing after acupuncture at tongue root points in healthy adults, as well as the central mechanism for the effect of acupuncture at tongue root points on swallowing function. Methods A total of 10 healthy young volunteers were enrolled, and functional magnetic resonance imaging was used to scan brain areas during the resting state, preparation for swallowing, and the process of swallowing before and after acupuncture at tongue root points. The datasets before and after acupuncture were analyzed to investigate the difference in activated brain areas during swallowing before and after acupuncture at tongue root points. Results Before acupuncture, the activated brain areas were mainly located in the left superior temporal gyrus and the right insular lobe, while after acupuncture, the activated brain areas were mainly located in the left posterior cerebellar lobe, the left cerebellar lobe, the left fusiform gyrus, and the right lingual gyrus, and the negative activated brain areas were mainly located in the left anterior central gyrus, the left posterior central gyrus, and the right posterior central gyrus. The differentially activated brain areas before and after acupuncture were mainly located in the left fusiform gyrus, the left middle temporal gyrus, and the left medial frontal gyrus, and the negative activated brain areas were mainly located in the left inferior parietal lobule. Conclusion Acupuncture at tongue root points affects the swallowing function possibly by enhancing the activity of swallowing-related brain areas in participating in swallowing and improving the execution efficiency of swallowing, thus achieving the goal of regulating swallowing muscle groups.