Speed profile design and tracking control are two important issues to ensure the performance of the automatic train operation system. Aiming to realize the maximum optimization probability of train running, this paper constructs an integrated optimal method through speed profile design and fuzzy PID controller design. In the recommended speed profile design, three typical running strategies are included in the proposed comprehensive scheme to extend solution space, and the constructed train performance simulation is combined with NSGA-II algorithm to solve such multiobjective problem. As for recommended speed profile tracking, in order to improve the tracking performance of the train, which is a nonlinear system, a fuzzy PID controller is designed to adaptively adjust PID gains. Note that multiple indicators of punctually, energy consumption, stopping accuracy and comfort are all considered in the integrated design. Taking Beijing Subway Line 8 as the numerical example, the results show that the design of speed profile and fuzzy PID controller are both effective, and energy consumption saves about 10.40% with other better indicators compared with the original data.