To predict the vibration characteristics of the crankshaft of the larger marine diesel engine accurately and comprehensively, based on the finite element models of the crankshaft and the engine block reduced by a component mode synthesis (CMS) method as well as extended Reynolds equation and Greenwood-Tripp theory, a mixed thermo-elasto-hydro-dynamic lubrication coupling model between a whole flexible engine block and a rotating flexible crankshaft is set up. According to this strongly coupled nonlinear model, the torsional-axial-lateral three-dimensional (3D) vibration of the crankshaft can be calculated simultaneously. The method is verified through comparison with other computational methods. Also, the vibrations are compared under different support models and whether to consider the effect of temperature. Specific 3D vibrations are displayed, and some stage nonlinear characteristics are shown in 3D direction. The modeling method will contribute to reveal the vibration mechanism and optimize the design of the shafting system.