Energy efficiency is paid more and more attention in railway systems for reducing the cost of operation companies and emissions to the environment. In subway systems, the optimizations on timetable and driving strategy are two important and closely dependent parts of energy-efficient operations. The former regulates the fleet size and the trip time at interstations, and the latter determines the control sequences of traction and braking force during the trip. Most conventional research optimized the timetable and the driving strategy separately such that global optimality cannot be achieved. In this paper, we analyze the hierarchy of energy-efficient train operation and then propose an integrated algorithm to generate the globally optimal operation schedule, which can get better energy-saving performance. Within the criteria of meeting the passenger demand, the integrated energy-efficient algorithm can simultaneously obtain the optimal timetable and driving strategy for trains, which realizes the combination of the high-level transportation management and the low-level train operation control. The simulation results based on the Beijing Yizhuang Subway Line illustrate that the integrated algorithm can achieve a 24.0% energy reduction for one day, on average. In addition, the computation time is within 2 s, which is short enough to be applied for real-time control system.