The prevailing configuration of train operation time parameters prioritizes line capacity utilization without considering variations in passenger flow distribution, leading to high traction energy consumption. To address this issue, this study proposes a refined configuration method for energy-saving train operation time parameters that incorporates passenger flow characteristics. First, the coupling relationships between “dwell time and passenger volume” at stations and among “passenger load, running time, and traction energy consumption” in sections are analyzed, based on passenger flow distribution differences between peak and off-peak hours. Subsequently, a configuration model is formulated with the objective of minimizing traction energy consumption per train cycle. An empirical study on a metro line demonstrates that, without extending the train turnaround time, the proposed method reduces traction energy consumption per cycle by 12.71% during off-peak hours and 6.69% during peak hours. These results confirm the energy-saving potential of the method, and the findings provide key parameters for generating energy-efficient timetables. The proposed approach is applicable to urban rail transit lines with distinct peak/off-peak passenger flow patterns.