For the end effect of empirical mode decomposition (EMD) in pace with the increase of the filtering level, a new improved method using a combination of extension with variable cosine window is proposed. Firstly, the signal is extended with a certain length of data. Then the extended signal is processed at both ends with variable cosine window before extracting the every Intrinsic Model Function（IMF）, which makes the end effect of each IMF minimized and ensures the correct decomposition and the improvement of the EMD algorithm. Simulation analysis and crack fault diagnosis example show that the improved method can inhibit end effect effectively.