In this paper, a new tribodynamic model for the translational joints with clearance is proposed by coupling the mixed lubrication model and the rigid-flexible multibody system dynamic model. The lubrication behavior is described by the average Reynolds equation and the Greenwood-Tripp asperity contact theory. Under a unified framework of the absolute nodal coordinate formulation (ANCF), motion equations of the rigid-flexible multibody system are established. The assembled equations of tribodynamic model are solved by a stable and effective algorithm. An application example of a two-stroke marine diesel engine is then used to study the tribological and dynamic behaviors of the crosshead-guide translational joint with clearance. The results show that considering the elastic deformation of components will lead to more intense secondary motion and smaller local clearance, resulting in an oil film pressure distribution with great difference from the rigid body modeling.