Compared with the previous model, a simplified mapping model of CRTS II slab ballastless track between pier settlement and the vertical deformation of rail was proposed based on Timoshenko’s beam theory. A cooperative finite element analysis model was established for verification purpose and the analysis of interlaminar stress. The results showed that the emergence of pier settlement causes the appearance of the void of the sliding layer between the base plate and the box girder above the piers, and the shear cogging reduces the void length to a certain extent. It was also observed that the rail is deformed cambered at the side pier (the pier with no settlement on both sides of the middle pier) and downwards at the middle pier (the pier with settlement). Moreover, the comparison between the theoretical value of the rail deformation and the finite element result demonstrated that the proposed mapping model can precisely characterize the relevant relationship. A conclusion also can be drawn that the pier settlement is attributed to the additional stress on the interface between the track slab and cement and asphalt mortar (CA mortar), and the interfacial stress is increased due to the effect of shear cogging.