The paper aims to solve the free-ride problem of supply chain members in view of the positive external market effect of agricultural product fresh-keeping investment. With the secondary fresh agricultural product supply chain as research object, a supplier-retailer fresh-keeping investment evolutionary game model under limited rationality was constructed. The dynamic evolution process of participant strategies was analyzed by the Jacobian matrix solution and MATLAB simulation. The supplier's and retailer's fresh-keeping investment strategy was closely related to the input and output benefits. When the parameters were in different threshold intervals, the system presented multiple evolutionary stable equilibriums. Factors such as the initial state of the game, market sensitivity and free-ride gains would also affect the formation of the system stable outcome. By analyzing the fresh-keeping investment strategies of fresh agricultural product supply chain members, it provides countermeasures and suggestions for improving the fresh-keeping level of fresh agricultural products.