In this paper, a simplified finite element model of the cracked crankshaft is proposed, and a new method for simulating the nonlinear vibration of operating crankshaft with several cracks is presented. For crankshaft, cracks occur frequently in the parts of crankpin-web fillet region and the edge of oil aperture because of fatigue or damage. According to the characteristic of those cracks, the cracked parts are modeled by the corresponding cracked spatial finite elements respectively, and two cracked elements are discussed in this study. The other, un-cracked, crankshaft parts are modeled by spatial Timoshenko beam elements. Flywheel and front pulley are simplified as lumped mass elements, and main bearings are simulated by equivalent linear springs and dashpots. In order to find the dynamic response of crankshaft-bearing system, a right-handed rotating coordinate system attached to crankshaft is applied. Based on the proposed finite element model, the breathing behavior of cracks in operating crankshaft is studied, and the nonlinear motion equation with variational stiffness is formed. Finally, a four-in-line crankshaft is taken as an example, and its vibration response corresponding to different kinds of crack are calculated and analyzed. Some conclusions are drawn, and a foundation is laid for diagnosing crack fault of crankshaft.