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To improve the energy-efficiency of transport systems, it is necessary to investigate electric trains with on-board hybrid energy storage devices (HESDs), which are applied to assist the traction and recover the regenerative energy. In this paper, a time-based mixed-integer linear programming (MILP) model is proposed to obtain the energy-saving operation for electric trains with different constraints of on-board HESDs, such as their capacity, initial state of charge (SOC), and level of degradation. The proposed integrated power flow model based on the train longitudinal dynamics, power split of on-board HESDs, and line impedance is discretized and linearized, aiming to minimize the net energy consumption (NEC). The results reveal that on-board HESDs with a higher capacity does not necessarily lead to a higher energy-saving rate; a lower or excessive initial SOC could undermine the energy-saving potential; considering the long-term train operation, the degradation of the Li-ion battery will influence the energy-saving operation for electric trains, as well as result in an energy-saving rate that ranges from 41.57% to 31.90%. The practical data from Guangzhou Metro Line 7 were applied in the simulations, which enhanced the practicality and effectiveness of the proposed method.