<p>Fairness concerns of enterprises will have a significant impact on the decision-making and profits of all parties in the supply chain. This paper introduces the fairness concerns psychological behavior of supermarkets, and establishes game models with 3PL mode and self-operated logistics mode respectively. Through Stackelberg game analysis, this paper analyzes the impact of fairness concerns on decision-making variables and utility of all parties. The findings of this study are as follows: Firstly, fairness concerns have changed the decision-making of all parties. Secondly, the wholesale price of cooperatives and the greenness of agricultural products both decline with the increase of fairness concerns under the two logistics modes. The sales price and logistics service level of supermarkets have different trends under the two logistics modes. Thirdly, with the increase of supermarket fairness concerns, the utility of supermarkets will increase first and then decrease with the 3PL mode; and the utility of supermarkets will increase with the increase of fairness concerns under the self-operated logistics mode. The utility of cooperatives has declined significantly under both logistics modes. Fourthly, without considering the fairness concerns of the supermarket, when the unit cost of self-operated logistics is low, if the unit cost of self-operated logistics exceeds that of 3PL, supermarkets will choose the 3PL mode. When the unit cost of self-operated logistics is very high, even if the unit cost of self-operated logistics is lower than that of the 3PL, the supermarket will still choose the 3PL mode. Fifthly, the fairness concerns of supermarkets have changed the choice of logistics modes. Supermarkets will choose 3PL mode only when the unit cost of the self-operated logistics is much higher than logistics cost of 3PL. And with the deepening of supermarket fairness concerns, the probability of cooperatives and supermarkets choosing self-operated logistics mode increases.</p>