This paper studied the application of virtual reality technology to the operation simulation of urban rail transit, aiming at enhancing the simulation effect and reducing the cost of development. Therefore, researchers can find the problems more accurately and quickly by concentrating on problem solving and operation optimization. A methodology for the simulation model construction was proposed based on multi-agent simulation technology and virtual reality system. Series of adaptive adjustments and improvements were made compared with the traditional method. A computer simulation model with a station as the scene was built. Experiment has been carried out to collect data for the simulation model validation. The results show that the methodology proposed in this paper is feasible and effective, which can provide support for the development of the virtual reality system of urban rail transit.