In order to improve train operation planning from the two perspectives of enterprise operating costs and passengers’ travel time, this paper proposes an integrated optimization model of three sub-problems, namely line planning, timetabling and rolling stock allocation for urban railway transit lines based on passengers’ travelling demands and the constraints of the urban rail line. The model features dwelling time at stations, turnaround operations at terminal stations, entering/exiting depot operations and an assignment for passengers’ travelling flow. We propose a solution method based on a metaheuristic method that simulates annealing to generate an optimal solution for the overall problem using MATLAB. Finally, we use the example of Xi’an metro line one to demonstrate the performance of the model.