Considering the intelligent train control problem in long-term evolution for metro system, a new train-to-train communication-based train control system is proposed, where the cooperative train formation technology is introduced for realizing a more flexible train operation mode. To break the limitation of centralized train control, a pre-exploration-based two-stage deep Q-learning algorithm is adopted in the cooperative train formation, which is one of the first intelligent approaches for urban railway formation control. In addition, a comfort-considered algorithm is given, where optimization measures are taken for providing superior passenger experience. The simulation results illustrate that the optimized algorithm has a smoother jerk curve during the train control process, and the passenger comfort can be improved. Furthermore, the proposed algorithm can effectively accomplish the train control task in the multi-train tracking scenarios, and meet the control requirements of the cooperative formation system.