This paper examines a high-speed railway CRTS-Ⅱ ballastless track-bridge system. Using the stationary potential energy theory, the mapping analytical solution between the bridge deformation and the rail vertical geometric irregularity was derived. A theoretical model (TM) considering the nonlinear stiffness of interlayer components was also proposed. By comparing with finite element model results and the measured field data, the accuracy of the TM was verified. Based on the TM, the effect of bridge deformation amplitude, girder end cantilever length, and interlayer nonlinear stiffness (fastener, cement asphalt mortar layer (CA mortar layer), extruded sheet, etc.) on the rail vertical geometric irregularity were analyzed. Results show that the rail vertical deformation extremum increases with increasing bridge deformation amplitude. The girder end cantilever length has a certain influence on the rail vertical geometric irregularity. The fastener and CA mortar layer have basically the same influence on the rail deformation amplitude. The extruded sheet and shear groove influence the rail geometric irregularity significantly, and the influence is basically the same. The influence of the shear rebar and lateral block on the rail vertical geometric irregularity could be negligible.