The separation of chaos and signal is an important problem of chaos signal processing. In recent years, the time-frequency analysis method is more and more mature. This paper first introduces the basic theory of time-frequency methods. We compare wavelet method with empirical mode decomposition (EMD) method, according to the different noise situation of the performance analysis of harmonic signal extraction in chaos background. Summarize a new synthesis about wavelet threshold and empirical mode decomposition (EMD) complementary of new harmonic signal extraction by experimental simulation. Computer simulation verified that the methods are high availability.