Timetable optimization is one of the effective solution methods for urban rail transit to achieve energy-saving. Previous studies on timetable optimization only focused on the transfer and utilization of mechanical energy, which did not consider the exchange of energy and line losses in the traction network. Therefore, this paper constructs a cross-substation energy transmission and utilization model taking into account the characteristics of the actual traction power supply systems. An overlap current method is presented to increase the utilization of regenerative braking energy (RBE) of trains and reduce the energy supply of the traction substation by considering the line loss, which is achieved by compensating the current generated by accelerating and braking trains in the substation. The compensation current can be maximized by adjusting the dwell time to achieve energy-saving. The traction power supply systems with highly nonlinear dynamic characteristics are linearized to construct a mixed-integer linear programming (MILP) model, which utilizes the utilization of RBE as the objection and dwell time as the variable. The method of maximum compensation current is verified by numerical examples based on Beijing Batong Line. The results show that the energy-efficient of the method is greatly improved compared with the method of maximizing the overlap time between the accelerating train and the braking train.