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Considering the carbon trading mechanism and consumers’ preference for low-carbon products, a game decision-making model for the low-carbon e-commerce supply chain (LCE-SC) is constructed. The influences of commission and carbon trading on the optimal decisions of LCE-SC are discussed and then verified through numerical analysis. On this basis, the influence of carbon trading on regional sustainable development is empirically analyzed. The results show that the establishment of carbon trading pilots alleviates the negative impact of unfair profit distribution. Increasing the commission rate in a reasonable range improves the profitability of LCE-SC. Nevertheless, with the enhancement of consumers’ low-carbon preference, a lower commission rate is more beneficial to carbon emission reduction. The total carbon emission is positively related to the commission rate. However, the unit carbon emission decreases first and then increases with the commission rate. The influence of the carbon price sensitivity coefficient on the service level is first positive and then negative, while the influence on the manufacturer’s profit goes the opposite. The empirical analysis confirms that the implementation of carbon trading is conducive to regional sustainable development and controlling environmental governance intensity promotes carbon productivity.