Aiming to minimize the total electricity usage in realistic operation of urban rail transit (URT) trains, this paper establishes the coupled model for the train-line-electric network-timetable (TLET) comprehensive system, and proposes a multi-train cooperative eco-driving method to achieve the system energy optimal. The dynamic power flow within the DC railway system with multiple trains is analyzed by modeling the traction power supply system (TPSS), and an improved power flow calculation (PFC) method is proposed to calculate the dynamic power flow distribution. To achieve the total substation energy minimization, a space-time-speed (STS) three-dimensional network is presented to transform continuous train motion process into discrete states on space-speed plane, and a multiple individuals dynamic programming (MIDP) algorithm is throughly developed to cooperatively optimize the multi-train trajectories along the time horizon, with which the optimal speed profiles and timetables of each train can be obtained simultaneously. Moreover, a computationally efficient heuristic algorithm together with a train-to-train (T2T) communication policy are developed as a comparative study. Numerical experiment with field data from Guangzhou Metro Line 8 is implemented, to illustrate the energy-saving performance of the proposed methods.