The purpose of this paper is to discuss how cross-border e-commerce enterprises can promote the sustainable development of the supply chain by optimizing the risk of supply disruption and product quality control mechanism of the cross-border supply chain of low-carbon agricultural products in the face of the problem of uneven quality and inventory shortage that prevails in the supply chain of low-carbon agricultural products under the framework of low-carbon economy. Methods: A two-level supply chain model consisting of a risk-averse cross-border e-commerce enterprise and two risk-neutral overseas suppliers is constructed to compare the optimal strategies and their coordination effects under the centralized and decentralized decision-making modes, and to deeply analyze the supply chain's operation mechanism. Further, the quality cost factor is introduced and an option contract model is designed to quantitatively analyze the impact of different decision-making scenarios and parameter changes on the overall supply chain performance. The results of the study show that under the coordination of option contract, the profit of cross-border e-commerce companies tends to decrease as the risk of supply disruption increases, while the profit of suppliers rises accordingly. Meanwhile, improving the quality of agricultural products can significantly improve the overall profitability of the supply chain. The cost-sharing mechanism is positively related to the profit of cross-border e-commerce companies, but negatively affects the profit of suppliers. In addition, the adjustment of the option price is directly associated with the increase of the specific supplier's profit and the decrease of the cross-border e-commerce enterprise's profit. Conclusion: By constructing and analyzing the option contract model considering the risk of supply disruption, this study effectively reveals the key influencing factors and their interactions in the cross-border supply chain of low-carbon agricultural products, and provides cross-border e-commerce enterprises with specific strategies to achieve coordination of the supply chain contract, improve product quality, and mitigate the risk of supply disruption, and then promote the sustainable development of the supply chain of low-carbon agricultural products.