Considering the decision-making requirements of airport, airlines and passengers, a bilevel programming model which contains two parts was proposed in this paper. One part is to improve the utilization of gates of the airport (upper level), so the objective function of the upper level to the minimum overall variance of slack time between two consecutive air crafts at the same gate. The other part looks at maximize the airline revenue and passengers more conveniently and comfortably (lower level). The lower level has two objective functions — the minimum passenger transfer failure and the minimum passenger average transfer time, respectively. According to the latest data of an airport in Eastern China, the adaptive genetic algorithm is used to solve the above-mentioned bilevel optimisation problems. The numerical experiment shows that the model not only reduces the variance of the relaxation time, but also optimises the flight gate allocation and achieves the initial goal.