This study examined the effects of TBS on suprahyoid motor cortex excitability and its potential mechanisms in healthy subjects. The findings demonstrated that TBS regulates suprahyoid motor cortex excitability, and its effects can last at least 30 min. Suppression of excitability in one hemisphere by cTBS led to further activation of corresponding contralateral motor cortex. Intermittent TBS eliminated the inhibitory effect induced by cTBS of the contralateral suprahyoid motor cortex. The effects of TBS on suprahyoid motor cortex and its potential mechanisms provide rationale for the therapeutic application.