Considering the peculiarities of logistics in the electronic commerce (e-commerce) supply chain (ESC) and e-commerce platform’s altruistic preferences, a model including an e-commerce platform, third-party logistics service provider, and manufacturer is constructed. Based on this, three decision models are proposed and equilibrium solutions are obtained by the Stackelberg game. Then, an “altruistic preference joint fixed-cost” contract is proposed to maximize system efficiency. Finally, numerical analysis is used to validate the findings of the paper. The article not only analyzes and compares the optimal decisions under different ESC models, but also explores the intrinsic factors affecting the decisions. This paper finds that the conclusions of dual-channel supply chains or traditional supply chains do not necessarily apply to ESC, and that the effect of altruistic behavior under ESC is influenced by consumer preferences. Moreover, there is a multiparty win–win state for ESC, and this state can be achieved through the “altruistic preference joint fixed-cost” contract. Therefore, the findings of this paper contribute to the development of an e-commerce market and the cooperation of ESC members.