Regional independent innovation, an important part of national innovation strategy, is the core of building an innovative country. Regional independent innovation system itself is a complex system, which is with clear self-organizing properties: openness, far from equilibrium, nonlinear, and fluctuate. This paper bases on self-organizing theory to study regional independent innovation system, which can enable us to further understand the formation and evolution of regional independent innovation system, and give us advices to enhance its capability.