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A railway transportation system is a typical spatio-temporal dynamic system. Cellular automata method is often used for road traffic flow research, but its homogeneity restriction makes it impossible to model railway transportation systems, because in railway transportation systems the objects cannot be divided into cells with same size and same transformation rule. Based on the research on railway transformation system's characteristics and cellular automata theory, the entity automata micro model is put forward in this paper. Entity automata divide the objects in railway transportation systems into several classes and every class entity has its own characteristics and transformation rule. It inherits the spatio-temporal computation characteristics of cellular automata and integrates object-oriented method. Simulation experiment result shows that it is feasible to model and simulate railway transportation systems by using entity automata.