The distribution of fresh agricultural products in our country is restricted by the ability of distribution, which causes too many intermediate links in the supply chain, so that the income of both ends in the supply chain (the suppliers of agricultural products and the final consumers) are seriously damaged. In this paper, with the help of matrix model analysis, we design a differentiated distribution mode for different suppliers. By using the method of dynamic game, we get the Nash equilibrium solution of the pricing and distribution time between the supermarket and the cooperatives in the Supermarket-oriented farm-supermarket direct purchase mode, and the conclusion is verified by an example. Finally, this paper also analyzes the change regularity of Nash equilibrium solution with the consumer demand for fresh agricultural products quality becoming more and more high, and puts forward the coordination mechanism in the development of distribution plan by the cooperatives and the supermarket to help the development of their core competitiveness.