A manufacturer-distributor-retailer supply chain is studied, and the impact on the supply chain operations caused by distributor’s fairness preference with the different reference points is examined. It is found that the whole supply chain’s profit is less than or equal to that as the distributor is complete rationality when the distributor has fairness preference with the downstream retailer’s profit as a reference point, but it is more than or equal to that as the distributor is complete rationality when the distributor has fairness preference with the upstream manufacturer’s profit as a reference point. Finally, a numerical simulation is provided to verify the correctness of the conclusion.