In order to reduce diesel engine vibration, low vibration optimization design was proposed based on empirical mode decomposition and time-frequency analysis. Firstly, Multibody Dynamics and finite element method was used to simulate the engine block vibration and the simulation results were verified by the test results very well.Then the empirical mode decomposition was used to decompose the vibration velocity signal of crankcase skirt. And the component of the decomposition results ,which has the largest vibration energy, was time-frequency changed by wavelet analysis. The time-frequency analysis results provided the main basis for structure optimization. At last, the vibration responses of the original block and the optimized structure were validated qualitatively by the wavelet analysis result and quantitatively by the Hilbert transform result.Results show that the vibrating intensity of the optimized block is reduced by 26.81% and the engine vibration is dramaticlly reduced. Therefore, it vertifies the effectiveness of the method.