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This paper, taking Changchun rail transit as an example, proposes a new method to simulate its running that is hierarchized simulation using timed discrete Petri and Simulink/Stateflow. Firstly, this paper uses the timed discrete Petri nets to build Changchun rail transit line 1-4 running model. And then, based on the timed discrete Petri nets model above, this paper also studies hierarchized simulation model by the tool of Simulink/Stateflow, which consists of two layers: the bottom layer is a single line model, and the top layer is a whole line model. In order to realize the rail transit running visualization, the tool of Matlab/App Designer is employed to design monitoring interface for Changchun rail transit line 1-4. This method is scalable and popularized.