The operations on the aircraft carrier flight deck are carried out in a time‐critical and resource‐constrained environment with uncertainty, and it is of great significance to optimize the makespan and obtain a robust schedule and resource allocation plan for a greater sortie generation capacity and better operational management of an aircraft carrier. In this paper, a proactive robust optimization method for flight deck scheduling with stochastic operation durations is proposed. Firstly, an operation on node‐flow (OONF) network is adopted to model the precedence relationships of multi‐aircraft operations, and resource constraints categorized into personnel, support equipment, workstation space, and supply resource are taken into consideration. On this basis, a mathematical model of the robust scheduling problem for flight deck operation (RSPFDO) is established, and the goal is to maximize the probability of completing within the limitative makespan (PCLM) and minimize the weighted sum of expected makespan and variance of makespan (IRM). Then, in terms of proactive planning, both serial and parallel schedule generation schemes for baseline schedule and robust personnel allocation scheme and equipment allocation adjustment scheme for resource allocation are designed. In terms of executing schedules, an RSPFDO‐oriented preconstraint scheduling policy (CPC) is proposed. To optimize the baseline schedule and resource allocation, a hybrid teaching‐learning‐based optimization (HTLBO) algorithm is designed which integrates differential evolution operators, peak crossover operator, and learning‐automata‐based adaptive variable neighborhood search strategy. Simulation results shows that the HTLBO algorithm outperforms both some other state‐of‐the‐art algorithms for deterministic cases and some existing algorithms for stochastic project scheduling, and the robustness of the flight deck operations can be improved with the proposed resource allocation schemes and CPC policy.