The subway and bus together contribute to the structure of public transport network in a metropolis. However, integrated service of public transport is not satisfied due to the lower timetable synchronization between these two modes at transfer stations. In this paper, a double-layer public transport network composed of subway/bus lines and stations is first created. Then, two stages are included in the timetable optimization process. In the first stage, a user equilibrium assignment model and a capacity restriction iterative algorithm are employed to obtain the passenger distribution in the subway–bus public transport transfer network. Based on this distribution, with the consideration of the synchronization and section service level, a mixed-integer linear programming (MILP) model is applied to optimize the timetables of the subway and bus networks in the second stage. Computational results using real Automatic Fare Collection System (AFC) data from the public transport system in Beijing are reported, and these results show that the suggested model is efficient in improving passenger service levels.