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Considering the interlayer height, luggage, the difference between queuing pedestrians, and walking speed, the pedestrian choice model of vertical walking facilities is established based on a support vector machine. This model is verified with the pedestrian flow data of Changchun light-rail transfer station and Beijing Xizhimen transfer station. Adding the pedestrian choice model of vertical walking facilities into the pedestrian simulation model which is based on cellular automata, the pedestrian choice behavior is simulated. In the simulation, the effects of the dynamic influence factors are analyzed. To reduce the conflicts between pedestrians in opposite directions, the layout of vertical walking facilities is improved. The simulations indicate that the improved layout of vertical walking facilities can improve the efficiency of pedestrians passing.