The accurate estimation of the rolling element bearing instantaneous rotational frequency (IRF) is the key capability of the order tracking method based on time-frequency analysis. The rolling element bearing IRF can be accurately estimated according to the instantaneous fault characteristic frequency(IFCF). However, in an environment with a low signal-to-noise ratio (SNR), e.g., an incipient fault or function at a low speed, the signal contains strong background noise that seriously affects the effectiveness of the aforementioned method. An algorithm of signal preprocessing based on empirical mode decomposition (EMD) and wavelet shrinkage was proposed in this work. Compared with EMD denoising by the cross-correlation coefficient and kurtosis(CCK) criterion, the method of EMD soft-thresholding (ST) denoising can ensure the integrity of the signal, improve the SNR, and highlight fault features. The effectiveness of the algorithm for rolling element bearing IRF estimation by EMD ST denoising and the IFCF was validated by both simulated and experimental bearing vibration signals at a low SNR.