Continuous theta burst stimulation (cTBS) is a non-invasive brain stimulation technique. cTBS modulation is an effective treatment for motor dysfunction rehabilitation in post-stroke patients. However, there's currently a lack of research on the effects of cTBS stimulation on the contralesional hemisphere. To better understand the role of cTBS in motor rehabilitation, we investigated the neuroregulatory mechanisms of cTBS in the contralateral cortex using transcranial magnetic stimulation-evoked electroencephalography (TMS-EEG). In this randomized, sham-controlled, single-blind study, 18 healthy subjects received two separate stimulation conditions:cTBS or sham stimulation applied to the left M1. TMS-EEG measurements were taken before and immediately after stimulation. We investigated the TMS-evoked potentials (TEPs), evoked oscillatory responses (EOR), and phase synchronization index(PSI) of TMS-EEG. The effects of cTBS were analyzed using two-way repeated measures analysis of variance (RMANOVA). There was a significant "cTBS condition×time" interaction effect on the theta and gamma bands of EOR, as well as on inter-hemisphere PSI (inter-PSI) and global PSI in both cTBS stimulation conditions. (theta:F=4.526,p=0.041;gamma:F=5.574,p=0.024;inter-PSI:F=5.028,p=0.032;global PSI:F=5.129,p=0.030).After real cTBS modulation, the energy in the theta and gamma frequency bands was significantly higher than before (theta: F=5.747, p=0.022; gamma: F=5.545, p=0.024). The inter-PSI and global PSI significantly increased after real cTBS modulation (inter-PSI: F=6.209, p=0.018; global PSI: F=6.530, p=0.015). cTBS modulation significantly increased EOR and PSI in contralateral brain regions, thereby enhancing cortical excitability and cortical functional connectivity throughout the brain. This provides a theoretical basis for cTBS neuromodulation in stroke patients.