The purpose of this research is to minimize the total cost of the overall system in the process of replenishment, to maximize the overall system profits. This paper regards all affiliated stores of chain supermarket as a system to do some research about the replenishment of fresh agricultural products. Then, this paper proposes the lateral replenishment strategy, analyzes its advantages, and applies the strategy thinking to the solution of the surplus or shortage of fresh agricultural products. Through the establishment of the inventory cost model, we compare the system inventory total cost between taking the lateral replenishment and deployment strategy and not using the lateral replenishment and deployment strategy, and get that there is lower total cost. Through the establishment of lateral replenishment transportation model, the optimal dispatching scheme between the surplus supermarket and the shortages supermarket is given. And then, the sensitivity analysis presents the variable range of the fresh agricultural products increment and decrement that does not affect this optimal dispatching scheme. This paper can provide a reference for the chain supermarket to deal with the shortage or surplus of fresh agricultural products so as to improve sales margins of agricultural products, to reduce the total inventory costs of the whole the chain supermarket system, and to improve the customer service levels.