Early studies have shown that Tai Chi Chuan (TCC) contributes to the rehabilitation of cognitive disorders and increases blood oxygen concentration levels in the parietal and occipital brain areas; however, the mechanism of TCC training on brain function remains poorly understood. This study hypothesize that TCC has altered brain function and aims to explore the effects of TCC on functional connection and effective connection of the prefrontal cortex (PFC), motor cortex (MC), and occipital cortex (OC). The participants were 23 experienced Chen-style TCC practitioners (TCC group), and 32 demographically matched TCC-naive healthy controls (control group). Functional and effective connections were calculated using wavelet-based coherence analysis and dynamic Bayesian inference method, respectively. Results showed that beyond the intensity of activity in a particular cortical region induced by TCC, significant differences in brain activity and dynamic configuration of connectivity were observed between the TCC and control groups during resting and movement states. These findings suggested that TCC training improved the connection of PFC, MC and OC in myogenic activity, sympathetic nervous system, and endothelial cell metabolic activities; enhanced brain functional connections and relayed the ability of TCC to improve cognition and the anti-memory decline potential.