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This paper is a study of the application of agent-based computational modeling method on the research of innovation system. The agent-based computational modeling method is applicable to research innovation system for it is suitable to describe relations and rules of the innovation members and innovation systempsilas complex feature, and it can simulate the real system to a certain extent. This paper regards the innovation system as a combination of enterprises, government, market, and society. Members in the system are linked by information. The model is programmed on Repast, and the test of competition to enterprisespsila innovation tendency is processed and analyzed.