<p>It has been widely known that the realization of carbon emission reduction requires the joint efforts of all stakeholders in the supply chain. The behavioral preferences of each stakeholder will impact the joint carbon emission reduction effect of the supply chain. However, the impact of altruistic preferences on stakeholders’ dynamic carbon emission reduction decisions has not been thoroughly studied. This paper develops differential game models considering a supply chain consisting of the manufacturer and the retailer and studies the optimal strategies of supply chain stakeholders under three different settings, i.e., the retailer altruistic model, the manufacturer altruistic model, and the cooperative model, respectively. Results demonstrate that the cooperative model has the highest level of manufacturer carbon reduction effort, followed by the manufacturer altruistic model and finally the retailer altruistic model. In addition, this research clarifies the pathway mechanisms by which the manufacturer can achieve a higher value chain position and more carbon emission reductions by exerting more efforts or adopting carbon reduction technologies with a low attenuation coefficient. This reveals a dynamic coupling mechanism between low-carbon transition and supply chain status reconfiguration. Furthermore, a larger carbon emission reduction attenuation coefficient is not only detrimental to sustained carbon emission reduction, but also detrimental to the manufacturer’s profit and the retailer’s profit. This paper provides a theoretical basis and practical reference for supply chain stakeholders’ joint carbon emission reduction decisions.</p>