The optimization of flight slot resources in airport networks aims to manage limited slot availability across various airports, waypoints, and flight segments, preventing conflicts at shared waypoints and thereby reducing delays. Key factors influencing airport network scheduling include airport and waypoint capacities, as well as transit flights, all interacting dynamically. This paper examines the impact of connecting flights and airport capacity uncertainty on scheduling, proposing a model to coordinate arrival and departure slots across the airport network. By meeting transfer time windows at each airport, the model allocates all flights to appropriate slots, minimizing both the total slot deviation and transfer wait times for connecting flights. The findings provide theoretical support for slot coordination and optimization for airports and airlines.