During the execution of flight schedule, the capacity of airport and airspace is often reduced by external dynamic factors such as weather conditions and flow control, which makes it impossible to meet the flow demand of airport and airspace, resulting in flight delay. In order to better implement tactical management of air traffic flow and reduce flight delay time and delay cost, this paper considers the impact of weather conditions, and combines ground and air waiting strategies to construct a multi-objective short-term flight time optimization model based on weather conditions, and uses NSGA-II algorithm to solve it. Finally, the Yangtze River Delta Airport Group is taken as an example to verify.