According to the frequency overlapping of intrinsic mode function (IMF) based on the temporal and spatial filtering of empirical mode decomposition (EMD), which will lead to the question of useful signals and noises filtered together, we proposed a method that numbers of IMF is determined by energy estimate, temporal and spatial filtering combing wavelet threshold and EMD integrating wavelet local signal characteristics of time and scale domain. This method not only used multi-resolution wavelet transform features, but also combined the EMD and Hilbert decomposition of the adaptive spectral analysis of instantaneous frequency and significance of the relationship between energy, so as to solve the problem of useful signal being weakened. With MIT/BIH ECG database standard data subjects, experimental results showed it was an effective method of data processing for handling this type of physiological signals under strong noise.