Non-stationary trend in R-R interval series is suggested to be removed to obtain reliable results for it could highly influence the frequency domain analysis of heart rate variability. In this study, three detrending methods, the smoothness prior approach, the wavelet and the empirical mode decomposition, were compared on artificial R-R interval series with four types of simulated trends. The Lomb-Scargle periodogram was used for frequency domain analysis. Results indicated that the wavelet method showed a better overall performance than the other two methods, and more time-saving, too. Thus the wavelet method is recommended as an optimal choice for use.