Collaborative innovation is a new way for innovation with minimum cost using enterprise capital and social capital. In a knowledge era, the outlook and frequency of innovation have changed. Collaborative innovation has become the mainstream for enterprise conducting innovation. Knowledge flow can provide assurance for innovation, so IP cooperation should be carried out between collaborative enterprises. For enterprise, how to make use of IP cooperation for collaborative innovation is an important issue that can ensure the smoothness of innovation. Based on the analysis of IP cooperation influential factors, a dynamic system model based on IP cooperation between collaborative enterprises is established. The cooperation efficiency is evaluated by simulation. Advices are given for improving IP cooperation efficiency in the process of collaborative innovation.