To systematically analyze the motivation pattern of innovation behavior and the impact of institution parameters, the issues and essential system parameters of intellectual property institution were analyzed. From the perspective of institution engineering theory, the system parameters of innovation behavior governance were analyzed taking intellectual property institution as an example. Based on model analysis and simulation, the findings include: the motivation pattern of innovation behavior is an integrated system consisted of multiple interlinked components and parameters. By virtue of the integrated adjustment of multiple key parameters including innovation cost, reimbursement, protective parameters, and punishment, it can encourage positive innovation, restrain intellectual property infringement and negative innovation. The side effect of over protection and inefficient protection can be offset. The policy reference for the motivation institutions of innovation behavior was proposed.