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To solve the problem of power quality (PQ) and neutral zone (NZ), a flexible traction power supply system (FTPSS) is proposed. This paper studies the energy management of FTPSS consisted of the hybrid energy storage system (HESS) and photovoltaic (PV). The model of battery degradation cost related to battery cycle depth is established, which is linearized by the piecewise linearization method. Based on traction load simulation data and PV prediction data, mixed-integer linear programming (MILP) model is established with the goal of minimizing the comprehensive cost. The comprehensive cost includes HESS degradation cost, PV operation and maintenance (O&M) cost, and electricity. The simulation results verify the significant economic-saving potentials of the proposed model in the FTPSS.