The analysis and evaluation of missile handling operation are crucial for ensuring safety and reliability during these processes. This paper proposes a novel assessment method for missile handling motions based on the Fuzzy Analytic Hierarchy Process (FAHP). The methodology comprises several stages: Initially, an analysis of missile handling motions is conducted. Subsequently, joint evaluation indicators influencing operational comfort are selected. Following this, membership functions and a comprehensive evaluation matrix are constructed. Finally, a fuzzy comprehensive evaluation model for the comfort level of carrier-based aircraft ammunition handling operations is established. A typical case study of carrier-based aircraft missile handling operation is presented to illustrate the fuzzy comprehensive evaluation process. The evaluation results are then compared with those obtained from the Rapid Upper Limb Assessment (RULA) and Ovako Working Posture Analysis System (OWAS) models. Comparative analysis indicates that the results derived from the fuzzy comprehensive evaluation model demonstrate high reliability.