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Through providing the new definitions of supply chain economy, market pertinent chain, operation link and interface link, we establish the supply chain economy model with electronic commerce based on variational inequality theory and spatial price theory. Furthermore, we have analyzed the characteristics and feasible conditions of cooperative innovation between supply chains, and added the cooperative innovation into the supply chain competition model. The results indicate that, through the cooperative innovation between supply chains, the large enterprise will inevitably promote the development of small enterprise, so every one wants to cooperative with a stronger enterprise. In other words, the cooperative innovation just can be in agreement between two enterprises with similar size.