A weapon system-of-systems (WSoS) is a higher-level system comprising various functional weapon equipment systems interconnected via mutual relationships, forming a hierarchical structure that can generate overall combat effectiveness. A critical factor in assessing WSoS performance is the kill chain, and quantifying the combat effectiveness of a WSoS based on the kill chain is crucial for optimizing the system’s structure and improving the understanding of the battlefield situation, holding significant military value. Scenarios involving restricted communication (e.g., limitations in weapon system capabilities, terrain obstructions, or enemy interference) make analyzing WSoS performance challenging, so proposed here is a kill chain-based method for analyzing WSoS capability in order to address the impact of communication restrictions. Specifically, a generalized multilayer network model with information relays is used to network the WSoS, then based on this, a capability-matrix-based method for generating and analyzing the kill chain is designed. Experiments show that the proposed model and method enable effective generation and analysis of the kill chain in communication-denial situations. Furthermore, a framework for evaluating WSoS performance is established from the dimensions of mission tasks and network structure, and combat effectiveness is assessed by quantifying performance indicators based on kill chain information. Finally, case studies are used to validate the proposed algorithm and show its reliability.