The dynamic simulation model of a threecylinder engine and the elastic hydrodynamic (EHD) lubrication model of main bearing were established using multibody dynamics method combined with finite element method (FEM). Then the constrained mode analysis for the composite structure of crankshaft system and engine body was conducted. The bending and torsional forced resonance frequency and modals of crankshaft system were further calculated and the following analysis focused on the bending vibration and shaft entire vibration that had more complex vibration modes. The experiments were finally conducted. The results show that the cause of crankshaft system torsional vibrations is its free torsional mode and the causes of bending vibration and shaft entire vibration are the constrained mode and the rigid mode of composite structure of crankshaft system  and engine body. The effect of bearing constraint on torsional mode is slight. The research brings the reference for the prediction and control of engine crankshaft system vibration.