The empirical mode decomposition（EMD） often suffers from the problem of mode mixing.Although the mode mixing can be alleviated to some degree by the ensemble EMD（EEMD）,but the introduction of assistant white noise in EEMD hinders time varying filtering performance of EMD. To enhance results of gearbox fault diagnosis,the time varying filter for EMD（TVFEMD） is introduced to examine gearbox vibration signals and a method for fault diagnosis of gearboxes based on TVFEMD is proposed. This proposed method is used to analyze the gearbox vibration data containing eccentricity of output shafts,the results show that the fault of eccentricity of output shafts of the gearbox can be effectively diagnosed,and a comparison between EMD,EEMD and TVFEMD indicates that the proposed method performs better in fault diagnosis of gearboxes.