Abstract: In e-commerce era, enterprises have begun to utilize e-marketplace to purchase more and more products and services so as to reduce transaction cost and increase the speed of market response. Therefore, stock-outs become an inevitable phenomenon. However, it is usually assumed that the losses resulted by stock-outs are afforded by the buyer. This paper proposes that supplier should make some compensation proportionally for buyer in case of stock-outs in e-marketplace transaction, so as to avoid the disaggregation of the supply chain system and realize win-win situation. Then, a model of compensation for stock-outs of supplier is established exploiting the principle of non-linear programming, and optimal solutions to order quantity are provided respectively.