The analysis of heart rate variability (HRV) has become a tool for noninvasively detecting the cardiovascular modulation of autonomic nervous system (ANS). Traditional analysis in frequency-domain mainly includes calculating the power and the peak frequency of each physiological frequency component. Whether employing the non-parametric or parametric method to estimate the power spectrum density (PSD), the approximate stationarity of HRV is presupposed. However, only in short-term analysis can data meet this condition. With the increase of the record time, the nonstationarity of HRV notably appears. A dynamic analysis method based on orthogonal wavelet transform was proposed in this paper, which not only can obtain the traditional indices in frequency-domain, but can compute their dynamic values varying with time, called short-time power and short-time LF/HF ratio. The latter can evaluate the activity of autonomic nervous system. Finally the method was applied to trace the balance of ANS in Atropin drug experiment.