To place emphasis on profound relations among airline schedule planning problems and to mitigate the effect of unexpected delays, we integrate robust schedule design, fleet assignment and aircraft routing problems within a daily planning horizon while passengers’ connection service levels are ensured via chance constraints and maintenance requirements are satisfied. We propose a nonlinear mixed integer programming model. In the objective function, the cost functions due to fuel consumption and CO2 emission cost involve nonlinearity. This nonlinearity is handled by second order conic reformulation. The key contribution of this study is to take into account the cruise time control for the first time in an integrated model of these three stages of airline operations. Changing cruise times of flights in an integrated model enables to construct a schedule to increase utilization of efficient aircraft and even to decrease the total number of aircraft needed while satisfying service level and maintenance requirements for aircraft fleeting and routing. Besides, for the robust schedule design problem, it is possible to improve the solution since a routing decision could eliminate the necessity of inserting idle time or compressing cruise time. In addition, we propose two heuristic methods to solve large size problems faster than the integrated model. Eventually, computational results using real data obtained from a major U.S. carrier are presented to demonstrate potential profitability in applying the proposed solution methods.