This paper analyses the dynamic behavior of a rail vehicle using experimental and simulation analysis on a multi-rigid–flex body model. The mathematical models are developed considering the car body, bogie frame, and wheel axle for rail vehicles of rigid–flexible and multi-rigid formulations, taking the car body as rigid for the rigid body analysis and the flexible car body for flex–rigid analysis. A finite element model of the car body was developed in ANSYS, and substructure and modal analyses were performed. The mathematical model is validated through an experiment conducted by the Research Design and Standards Organization. Then, the validated model is further analyzed to evaluate the running comfort, using the Sperling ride index and the running safety, by investigating the derailment coefficient and wheel load reduction rate. The impact of flexibility on the vehicle’s running stability is investigated using the rigid body dynamics model and experimental data. Compared to experimental data, the simulation results reveal that elastic vibration cannot be neglected in vehicle dynamics, since the rigid–flexible coupling model is slightly more significant than the rigid-body model for ride comfort and safety.