In order to improve the control performance of automatic train operation (ATO) in urban rail trains, five typical operating sequences of urban rail trains were studied. Under the condition of meeting the safety and comfort principles of train operation, a train dynamics model was established to achieve the goals of low energy consumption, short running time, and high stopping accuracy in urban rail transit trains. In the process of finding a multi-objective solution to this problem, the Non-dominated Sorting Genetic Algorithm II (NSGA-II) was used with an elite retention strategy, and the optimal Pareto multi-objective solution set was sought. In the process of optimal solution weight assignment, the hierarchical analysis Mahalanobis distance method, which combines subjective and objective analysis, was used. Finally, taking the Beijing Yizhuang subway line as the background design example, the simulation verified the effectiveness and feasibility of the algorithm and obtained high-quality automatic train driving curves under various working conditions. This research has important reference significance for the actual operation of automatic driving in urban rail trains.