Empirical mode decomposition (EMD) is widely used in mechanical fault diagnosis, but its inevitable mode mixing in EMD exerts an influence on effectiveness. Mode mixing in EMD is studied, and two kinds of causes leading to mode mixing are found. One caused by the basic principle of EMD is called type-I mode mixing, such as mode down mixing and mode cross mixing, the other caused by faults of the sifting process is called type-II mode mixing, such as mode upward mixing. The improvement schemes are proposed according to the different mode mixings. For type-I mode mixing ，some supplemental measures such as abnormal event elimination, signal filter and supplemental signal added method are necessarily introduce in problem solving. For type -II mode mixing, the definition of intrinsic mode function is perfected, and the sifting process is improved. The simulating results show that the proposed schemes are effective.