In this study, a promising nonlinear method, termed the principal dynamic mode (PDM) method, is used to separate dynamic components of the sympathetic and parasympathetic nervous activities based on ECG signal, and the results are compared to the power spectral approach to assess the ANS balance. The PDM analysis based on the 28 subjects consistently resulted in a clear separation of the two nervous systems, which have similar frequency characteristics for parasympathetic and sympathetic activities as those reported in the literature. With the application of atropine, in 13 out of 15 supine subjects there was an increase in the sympathetic/parasympathetic ratio (SPR) due to a greater decrease of parasympathetic than sympathetic activity (p=0.003), and all 13 subjects in the upright position had a decrease in SPR ratio due to a greater decrease of sympathetic than parasympathetic activity (p<0.001) with the application of propranolol. The low frequency/high frequency (LF/HF) ratio calculated by the power spectral density is less accurate than the PDM because it is not able to separate the dynamics of the parasympathetic and sympathetic nervous systems. The culprit is equivalent decreases in both the sympathetic and parasympathetic activities irrespective of the pharmacological blockades. These findings suggest that the PDM shows promise as a noninvasive and quantitative marker of ANS imbalance, which has been shown to be a factor in many cardiac and stress related diseases.