•Tai Chi mind–body exercise was compared to brisk walking aerobic exercise on modulating the interactions between heart rate variability (HRV) and blood flow oscillations (BFO) of the upper and lower limbs.•Tai Chi is effectively on modulating the degree of coherence between HRV and BFO of the upper limb.•Brisk walking is effectively on modulating the degree of coherence between HRV and BFO of the lower limb.•Wavelet phase coherence between HRV and BFO is able to differentiate the effect of mind–body exercise from aerobic exercise. Tai Chi exercise has been demonstrated to be beneficial for health and quality of life. However, the mind–body effect of Tai Chi on modulating interactions of the cardiovascular components has not been investigated. This study aimed to differentiate the effect of Tai Chi (mind–body exercise) and brisk walking (aerobic exercise) on modulating skin blood flow oscillations (BFO) of the upper and lower limbs and heart rate variability (HRV). Bafa Wubu of Tai Chi for 15 min and brisk walking for 15 min were performed by 30 adults in two different days. Wavelet phase coherence was employed to assess the coordination between HRV and BFO before and after exercise. Two indices were proposed to quantify the coherence, i.e., the area (Aϕ) and maximal difference (dmax) between the coherence function and the threshold obtained by surrogate test. The results demonstrated that Tai Chi resulted in a significant decrease in phase coherence between HRV and BFO of the upper limb in the frequency interval 0.05–0.15 Hz (Aϕ baseline 0.1600 ± 0.0288, post-exercise 0.0486 ± 0.0220, p < 0.001; dmax baseline 0.3222 ± 0.0220, post-exercise 0.2578 ± 0.0219, p < 0.005), but not between HRV and BFO of the lower limb. Brisk walking resulted in a significant increase in phase coherence between HRV and BFO of the lower limb in the frequency interval 0.05–0.15 Hz (Aϕ baseline 0.0455 ± 0.0251, post-exercise 0.1190 ± 0.0241, p < 0.05; dmax baseline 0.2191 ± 0.0225, post-exercise 0.3103 ± 0.0208, p < 0.05) but not between HRV and BFO of the upper limb. Our finding indicates that mind–body exercise and aerobic exercise modulate cardiovascular regulations through different mechanisms of action.