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Non-functional requirements are emerging as one of the most crucial factors for successful information system development in service-oriented organizations. Non-functional requirements involve not only software characteristics but also numerous organizational elements. This study proposes a conflict analysis method for non-functional requirements of information systems. This method includes ontologies, metadata, and rules. The domain independent ontology is derived from software engineering and business management field. The ontology includes software attributes, business values, and restrictions. The metadata can be filled in with concepts from ontology to model a non-functional requirement. The rules reveal the contradiction between non-functional requirements based on ontology and metadata. Finally, this study provides examples to demonstrate and validate this method. In the expectation, this method can facilitate the organization to pay attention to contradicted non-functional requirements of information systems and handle them more effectively.