Semi-active suspension technology can improve the overall dynamic performance of rail vehicles in different aspects and is much safer and more cost-effective than the full-active suspension for practical implementation. Magnetorheological (MR) damper is a promising technology among the other alternatives, considering its compact dimension and fast response time, which allows easy replacement of the passive damper to control vibration at a relatively high-frequency range. This work performs characterization tests of a prototype MR damper to investigate its dynamic performance. A nonlinear dynamics model is proposed to reproduce the behaviour of the MR damper, particularly on elasticity of the rubber end mounts. The model parameters are calibrated showing excellent agreement with the experimental test. Based on the accurate MR damper model, the dynamics and control of the MR damper are studied in the application of semi-active primary suspension (SAPS) to improve vertical ride comfort. The proposed control scheme can significantly improve vertical ride comfort, particularly effective in controlling car-body first bending vibration. The study on the elasticity of damper end mounts also provides suggestions to refine the property of the MR damper and improve the control effect.