Express delivery in rural areas of China has many problems, such as high delivery cost and low efficiency. As an effective way to solve the difficulties of rural delivery, it is important to study the innovation and application of a joint distribution model. In the background, this paper takes express delivery enterprises in rural areas as the research object. First, it proposes to construct a three-level “county-town-village” joint distribution system in which e-commerce platforms participate. Next, it establishes an evolutionary game model of express delivery enterprise joint distribution alliance and solves it. Finally, the model is analyzed through numerical simulation. The results show that the distribution system of express delivery enterprises in rural areas is affected by excess returns, early input costs, operating costs, cooperation risks, penalty costs, learning and absorption capacity of enterprises and other factors. After introducing the rewards and punishments of e-commerce platforms as an independent influencing factor in the evolutionary game model, the shorter time for express companies to finally make cooperation strategies indicates that the rewards and punishments of e-commerce platforms have a positive significance in promoting the rapid development and stable operation of a rural logistics joint distribution system.