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This paper concerns the new development in multi-agent based enterprise software engineering practices, systematically discusses the main issues and approaches towards successful enforcement of complex agent-oriented software engineering, related to multi-agent system (MAS) organization structure design, ontology based domain knowledge representation and put forward an ontology based MAS coordination architecture. This paper mainly focuses on multi-agent approaches to enterprise legacy system evolution, intelligent integration and coordination design, not on specific agent architectures. Organization structure design provide MAS long-term system guidelines, together with the ontology-based domain knowledge structure and relationship representation, that provide the agents structure and environment description for MAS coordination mechanisms, also this paper gives a fundamental ontology-based agent communication interface definition. As a case study, this paper analyses China deregulated power industry information system integration requirements, apply MAS organization design approaches in electric power decision support application system MAS architecture design, and suggests CIM/XML as a standard criteria to ontology-based electric power domain knowledge management for multi-agent resources sharing, reuse and coordination.