A new fault diagnosis method to suppress cross terms of Wigner-Ville distribution (WVD) using Adaptive Short-time Fourier Transform (ASTFT) spectrum is put forward. The relationships of correlation between auto terms and cross terms of WVD are obtained theoretically by analyzing the WVD. Firstly, the signal ASTFT spectrum which can determine the signal component positions in the time-frequency plane is obtained. Then, the ASTFT spectrum as a window function is selected to process the signal WVD. Thus the cross terms can be effectively restrained. The simulation results show that a better resolution and more effective suppression of cross terms can be obtained. At last, the proposed method is applied to the fault diagnosis of bearing. The simulation and the experiment results indicate that the proposed method is effective in feature extraction.