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Continuous theta-burst stimulation (cTBS) induces long-lasting inhibitory effects on cortical excitability. Although cTBS has been reported to modulate neural oscillations and functional connectivity, it is still unclear how cTBS affects brain dynamics that could be captured by the resting-sate EEG microstate sequences. This study aims to investigate how cTBS over the left motor cortex affects brain dynamics. We applied 40 s-long cTBS over the left motor cortex of 28 healthy participants. Before and in multi-sessions up to 90 min after cTBS, their performance in a Nine-Hole Peg Test (NHPT), that measures the hand dexterity, and resting state EEG were recorded. Resting-sate EEG data were clustered into four microstates (namely A, B, C, and D) using k-means clustering algorithms. cTBS-induced changes in NHPT performance, microstate dynamics and functional connectivity networks were comprehensively assessed. As compared with baseline, the completion time of NHPT became shorter immediately after cTBS, suggesting cTBS-induced motor function improvement. After cTBS, the topography of microstate B revealed a greater change compared with other three topographies. Importantly, cTBS-induced decrease in completion time of NHPT correlated with cTBS-induced decrease of the mean occurrence of microstate B. Functional connectivity analysis further revealed that cTBS led to an increase of the node efficiency at C4 electrode in microstate B. These results indicated the specific modulation of cTBS over the motor cortex on the dynamics of microstate B. This work provided the evidence of the association between B and motor function, and it also implies the modulation of cTBS over the motor network. [ABSTRACT FROM AUTHOR]