The intelligent upgrading of metropolitan rail transit systems has made it feasible to implement demand-side management policies that integrate multiple operational strategies in practical operations. However, the tight interdependence between supply and demand necessitates a coordinated approach combining demand-side management policies and supply-side resource allocations to enhance the urban rail transit ecosystem. In this study, we propose a mathematical and computational framework that optimizes train timetables, passenger flow control strategies, and trip-shifting plans through the pricing policy. Our framework incorporates an emerging trip-booking approach that transforms waiting at the stations into waiting at home, thereby mitigating station overcrowding. Additionally, it ensures service fairness by maintaining an equitable likelihood of delays across different stations. We formulate the problem as an integer linear programming model, aiming to minimize passengers’ waiting time and government subsidies required to offset revenue losses from fare discounts used to encourage trip shifting. To improve the computational efficiency, we develop a Benders decomposition-based algorithm within the branch-and-cut method, which decomposes the model into train timetabling with partial passenger assignment and passenger flow control subproblems. We propose valid inequalities based on our model's properties to strengthen the linear relaxation bounds at each node of the branch-and-bound tree. Computational results from proof-of-concept and real-world case studies on the Beijing metro show that our solution method outperforms commercial solvers in terms of computational efficiency. We can obtain high-quality solutions, including optimal ones, at the root node with reduced branching requirements thanks to our novel decomposition framework and valid inequalities. Our integrated optimization approach reduces the fleet size for operators by at least 8.33 % and decreases the waiting time of passengers on the tested instances, thereby validating the effectiveness of our proposed methods.