In modern amphibious operations, vertical landing has gradually become the mainstream approach for force projection due to its flexibility, mobility, and rapid response capabilities. The flight deck operations of carrier-based aircraft have also garnered increasing attention. Addressing the inefficiencies in scheduling flight deck operations under complex mission scenarios aboard amphibious assault ships, this study analyzes the characteristics of such operations and the deck environment. A scheduling model is developed with the objective of optimizing the support operation cycle, and a modified greedy algorithm based on a sliding time window strategy is proposed for solving the model. By dividing the entire support operation time into several fixed time windows, the algorithm determines the optimal scheduling plan within each time window, thus enabling carrier-based aircraft to execute phased projection missions efficiently. Finally, a simulated case study of amphibious projection operations is conducted to validate the proposed method. The simulation results demonstrate the feasibility and superiority of the scheduling method.