Combining refined passenger demand optimization with intercity train timetables holds significant practical value in promoting the public transport operation of intercity trains. Under specified refined passenger demand conditions, the model takes into account key constraints related to train operations, passenger boarding and alighting processes, as well as the statistical data on passengers boarding and alighting. This comprehensive approach ensures the safety and efficiency of train operations. Moreover, the study introduces a system cost calculation formula that incorporates both the total cost of the railway department and the total cost of passenger travel. The goal is to minimize the system cost while constructing a non-linear optimization planning model that considers intercity train cross-station operations and rational adjustments of train departure intervals. The solution to this model involves the utilization of the simulated annealing algorithm. To validate the efficacy of the model and algorithm, a case study is conducted on a specific intercity line during a weekday morning peak period. The results demonstrate that the optimized timetable leads to a reduction of 11.5% in system costs, a 7.5% decrease in the total cost incurred by the railway department, and a 13.45% decrease in the total cost of passenger travel. This highlights the potential of strategies such as flexible train stops and rational adjustment of train departure intervals as valuable references for achieving a public transport operation of intercity trains, especially under refined passenger demand conditions.