Aiming at the problems of punctuality, parking accuracy and energy saving of urban rail train operation, an intelligent control method for automatic train operation (ATO) based on deep Q network (DQN) is proposed. The train dynamics model is established under the condition of satisfying the safety principle and various constraints of automatic driving of urban rail train. Considering the transformation rules and sequences of working conditions between train stations, the agent in the DQN algorithm is used as the train controller to adjust the train automatic driving strategy in real time according to the train operating state and operating environment, and optimizes the generation of the train automatic driving curve. Taking the Beijing Yizhuang Subway line as an example, the simulation test results show that the DQN urban rail train control method reduces energy consumption by 12.32% compared with the traditional train PID control method, and improves the running punctuality and parking accuracy; at the same time, the DQN train automatically driving control method can adjust the train running state in real time and dynamically, and has good adaptability and robustness to the change of train running environment parameters.