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In an open environment, there are a large number of agents based on different semantics which caused inconvenience in collaboration each other as well as difficulties in multi-agent system modeling. Considering multi-agent system in the communication, collaboration, knowledge sharing and other characteristics, an ontology-based multi-agent system model for large-scale structural damage identification was proposed by reducing the complexity of the system, which can get the same semantic between heterogeneous agents through ontology mapping based on the model. With the proposal of the system framework, the problem-solving knowledge bank based on ontology and a functional verification system for airplane wing's aluminum structure were both designed. The results show that ontology can get achievement in collaboration among the agents, and the system can also locate the large-scaled structure damage automatically.