To alleviate peak-hour congestion in urban rail transit, this study proposes a new off-peak fare discount strategy to incentivize passengers to shift their departure time from peak to off-peak hours. Firstly, a questionnaire survey of Shanghai metro passengers is conducted to analyze their willingness to change departure time under different fare strategies. Secondly, based on the survey results, a time-differentiated fare discount model is constructed, considering both the company’s revenue and passengers’ travel benefits, and with the optimization objective of achieving balanced peak-hour and off-peak-hour train loads throughout the day. Subsequently, a genetic algorithm with nested fmincon functions is designed and combined with the actual data of Shanghai rail transit line 9 for arithmetic analysis. Finally, the effectiveness of the model is validated using the survey data. The research results show that the off-peak fare discount strategy can incentivize 6.88% of passengers traveling in the morning peak and 6.66% of passengers traveling in the evening peak to shift to off-peak travel. This research provides theoretical support and decision-making guidance for implementing time-differentiated pricing in urban rail transit systems.