Analysis of heart rate variability (HRV) is widely used for noninvasive assessment of the state of the regulation systems of the heart. The aim of this study was to evaluate the capabilities of the Hilbert-Huang method for calculating spectral parameters of HRV in comparison with the commonly used Fourier analysis. Fourier analysis allows estimation of averaged spectral amplitudes and power of HRV oscillations in fixed frequency intervals, which are associated with the activity of sympathetic, parasympathetic, and humoral regulation systems. Using the Hilbert-Huang method, we revealed four spectral components, described by Gaussian functions, in which HRV oscillations are concentrated, and showed the absence of fixed boundaries between them. The obtained energy quantitative characteristics of the spectral components of heart rhythm oscillations can serve as the basis for diagnostic methods of heart rhythm regulation, supplementing the commonly used ones.