The efficiency of ammunition support operations in the aircraft carrier intermediate ordnance staging deck is critical to sortie generation rates in naval aviation, yet joint scheduling and personnel allocation in this multistage, resource-constrained environment remains a challenging bi-objective optimization problem. This study develops a framework integrating an improved Nondominated Sorting Genetic Algorithm II (NSGA-II) with a marginal-benefit-based iterative feedback mechanism. The intermediate ordnance staging deck support process is decomposed into individual ammunition processing stations and formulated as a processflow model incorporating operation sequencing and personnel specialization constraints. A constraint decision model then dynamically reconciles the minimization of total makespan and personnel workload equilibrium through iterative marginal-benefit comparison across support teams. The NSGA-II is enhanced with an adaptive crossover-mutation mechanism and an improved elitism preservation strategy to strengthen global search capability. Validation on a typical carrier intermediate ordnance staging deck scenario demonstrates that the improved NSGA-II outperforms the conventional NSGA-II in convergence speed and Pareto front quality. Under the optimized configuration, the total makespan remains 3600 s with a workload balance metric of 1075 even as ammunition quantity doubles from two to four units. The proposed framework offers practical decision support for carrier ammunition operations and extends to other resource-constrained multi-objective scheduling domains.