This paper builds a theoretical framework of mechanism for rural e-commerce to promote the collaborative innovation of agricultural industry clusters from the accumulation of resources such as production factors after the development of rural e-commerce in agricultural industry, the overflow of knowledge, the reconstruction of relationship networks, and the creation of an innovative environment. Taking the characteristic agricultural industry of Mile in China as an example, the mechanism of rural e-commerce to promote collaborative innovation of agricultural industrial clusters was explored. A good agricultural industry foundation is the advantages and potential of developing e-commerce, and the development of rural e-commerce can better promote the integration of resource of agricultural industry clusters and enhancement of innovation capabilities.