Based on "Farmer-Supermarket Direct-Purchase" as the research background, with farmer, supermarket, logistics company as the main body of research, this paper combines with the thoughts of contract theory, introduces the concept of fresh-keeping contract of agricultural products. Then, using game theory to analyze whether to sign the fresh-keeping contract between the supermarket and farmer, supermarket and logistics company. The results indicate that: when farmer and supermarket sign the fresh-keeping contract of fresh agricultural products, the farmer and the supermarket will both benefit from the fresh-keeping contract. Whether supermarket and logistics company sign the fresh-keeping contract is determined by w1, w2 . If w1=w2, the supermarket and the logistics company can sign the fresh-keeping contract or cannot sign a contract. If w1＞w2, supermarket and logistics company will not choose cooperation. If w1＜w2, as long as the liquidated damages is in a reasonable range, supermarket and logistics company will both benefit from signing a fresh-keeping contract. This paper can provide a reference for the supermarket, farmers, logistics companies when sign fresh-keeping contracts.