To address the limitations of traditional command paradigms in naval integrated air and missile defense (IAMD), this paper develops a doctrine-compliant modeling and simulation framework that integrates hierarchical colored Petri nets (HCPN) with ZhuYuanWarSim™—an autonomous combat simulation platform developed in-house for high-fidelity command process emulation. The framework formalizes three-layer command logic—strategic intent propagation, operational task decomposition, and tactical coordination—ensuring compliance with standardized air defense protocols. ZhuYuanWarSim™ enables high-fidelity battlefield emulation through hybrid time synchronization and dynamic threat injection. Experimental validation under saturation attack scenarios demonstrates mission command’s superiority over centralized C2 across three dimensions: enhanced command efficiency through optimized decision pathways, improved network survivability under node attrition, and reduced kill chain closure timeline. Monte Carlo simulations (N = 100 trials) with randomized communication delays and node failures confirm the robustness of these advantages. The structurally adaptable modular architecture ensures cross-domain operational command chain analysis, establishing a universally applicable framework for evaluating decentralized C2 systems in complex combat environments.