IUR cooperation is the strategy union consisting of the enterprises as the regional innovation main-body which has the perception ability of market demand and the university, scientific research institutions which have the knowledge reservation, scientific research equipment and innovation team under knowledge-economic situation to?achieve?resource?sharing?and?advantage?complementation. This paper starts from perspective of the resource dependence theory, analyzes the operation mode and dynamic mechanism in the regional innovation system construction. The conclusion is that IUR cooperation shall be based on the market demand as the guide, the technological innovation cooperation by enterprise as the main body as the mode, the inter-subjective resource dependence as the power mechanism. The study is of important theoretical significance and the practical significance to improve regional innovation ability.