This paper investigates flight delay propagation in the air transport networks. An integrate flight-based susceptible-infected-susceptible (FSIS) model is generated using the mechanism of epidemic spreading. Furthermore, the propagation probability in the FSIS model is analyzed through the regression model and later applied to China Easter Airline. The results show that propagation probability varies from different routes, which related to the flight frequency of airports, route distances, scheduled buffer times, and propagated delay times, and the FSIS model can efficiently reveal the process of flight delay propagation, and evaluate the number of delayed flights.