In order to analyze the operational efficiency and the robustness of flight scheduling, computer simulation technology was applied to air transport system in this paper, and a flight operation system model which contains 118 major domestic airports was constructed based on Flexsim simulation software. The model implemented the flight scheduling operation of a large-scale airline by simulating the aircraft operation processes of take-off/landing, taxiing in/out, flight turnaround ground service, and segment flying. Parameters of several aircraft operation time were set by combining the classification method and different fitting distributions, such as fitting flight turnaround time with Logistic distribution. This system model could simulate flight operation under normal condition and abnormal condition (e.g., flow control), as well as export evaluation indexes, such as delay time, punctuality rate, aircraft utilization rate, and buffer time gap. Case analysis was validated to demonstrate the performance of the model and it showed that the model could accurately simulate the actual operation of airlines’ flight. Under normal condition, the key points of flight delays could be determined with the analysis of output indexes, whereas under flow control the transmission mode of delays were found to be passing down along the flight string as the delay time reduced gradually, and the turnaround time of directly affected flights was increased, while that of indirectly affected flights was reduced at the same time.