Abstract: A new method called generalized Multi-Window S-Transform (MW-ST) is proposed for blind Instantaneous Frequency (IF) analysis of complex emitter signals. The high concentration is achieved by employing the modified Hermite function. In this distribution, the orthogonal Hermite function is improved by utilizing a frequency parameter. Therefore, the multi-window method can be introducing to S-transform. The generalized MW-ST maintains the multi-resolution characteristics of the ST and improves the frequency resolution in high frequency region. Comparing with the origin S transform and the multi-window method, the proposed method can effectively improve the accuracy of the IF estimation and the time-frequency concentration. So it has the good prospects for engineering applications.