Previous studies have explored the relationship between the complexity of local blood flow signals and heart rate variability (HRV) under different thermal stimulations. However, the relationship between the complexity of local blood flow signals and HRV in different positions is not clear. In this study, healthy participants were placed in different body positions. The bilateral blood flux and ECG were monitored, and refined composite multiscale entropy (RC MSE) and refined composite multiscale fuzzy entropy (RC MFE) were used to measure the complexity of the local blood flux. The sample entropy was calculated to evaluate the HRV complexity. The change of body position did not affect the time domain or frequency domain of HRV, but did reverse the blood flux laterality of the lower extremities. Furthermore, there was a negative correlation between the complexity of right-side blood flux and sample entropy of HRV when the participant was in the -10 degrees position. These results provide a new perspective of the relationship between skin blood flux signals and cardiac function.