With the development of modern military ship equipment, the airspace operation environment of shipboard aircraft is becoming increasingly complex. The objective and accurate evaluation of ship-terminal capacity is the basis of air traffic flow management for shipboard aircraft, and it is also the premise of improving the efficiency of airspace resources. First of all, this paper divides the airspace and ship terminal areas and realizes the route network planning for the arrival and departure of shipboard aircraft. Following this, according to the airspace characteristics of the ship terminal area and the operation process of the shipboard aircraft, an arrival-and-departure network flow model for shipboard aircraft is established by using capacity-limitation and flow-conservation conditions. Finally, simulated annealing (SA) is used to solve the maximum flow in the arrival-and-departure network flow model, and the capacity evaluation results of the ship terminal area are obtained. The results show that when the number of gates is ng≥ 7, the bottleneck in the ship terminal area’s operation capacity is the deck runway. When 3 ≤ ng < 7, imbalanced take-off and landing tasks lead to a waste of runway resources, and when ng < 3, the number of gates becomes the bottleneck which limits the capacity. With the number of gates being reduced from seven to three, the capacity is reduced from twenty sorties per hour to six sorties per hour. The model and core idea proposed in this paper can not only quickly evaluate the capacity of the terminal area of ships but also provide a solid foundation for the development of future fleet groups and the full use of maritime airspace.