In order to relieve the issue of persistent capacity strain in the main passenger flow direction and significant underutilization in the non-main direction caused by tidal passenger flow, a flexible express skip-stop strategy was proposed, based on asymmetric train operation patterns for a dual-depot double-line metro system to optimizing the train schedule during peak hours. The objective function aims to minimize both total passenger waiting time and train dwell time. A mixed-integer nonlinear programming model was formulated, integrating constraints related to timetables, flexible skip-stop operations, rolling stock circulation, and passenger flow balance. A hybrid algorithm combining genetic algorithm and simulated annealing was developed to solve the proposed model. The coordinated optimization of train schedules, stop plans, and rolling stock circulation plans was achieved. Finally, the validity of the model and algorithm was verified through a case study of Jinan Metro Line 3. The optimization outcomes of three operational schemes: symmetric operation, flexible skip-stop, and a combined approach integrating asymmetric operation with flexible skip-stop were compared. The results show that the combined asymmetric transportation strategy and flexible skip-stop approach reduces passenger waiting time by 3.43%, shortens train dwell time-related duration by 10.93%, and lowers the objective function value by 7.56%.It is concluded that the proposed asymmetric transportation strategy combined with a flexible skip-stop operation scheme effectively addresses tidal passenger flow phenomena, enhances operational efficiency and service quality during peak hours in urban rail transit, and provides new insights and references for optimizing operational management.