In this study, the influence of external noise on heart rhythm variability (HRV) in nonlinear dynamic analysis and the internal stochastic factor of HRV were discussed in connection with their physiological significance. The sampling rate, stationary and non-uniformity time interval were analyzed. An interpolation algorithm for heart period was introduced. The experiment demonstrated that the influence was highly reduced by the mentioned procedure. The internal stochastic factors of HRV were investigated by several nonlinear dynamic methods such as surrogate data, mutual information and nonlinear forecasting. The results suggested the colligation of deterministic chaos and stochastic process should be a favorite to interpret HRV.