As cross-border e-commerce platforms become increasingly integrated into the agricultural supply chain, the establishment of a sustainable supply chain ecosystem is of paramount importance. This study, grounded in the platform theory and the supply chain ecosystem theory, combines the grounded theory and the DEMATEL-ISM-MICMAC model to thoroughly analyze the complex mechanisms driving sustainable development. Utilizing the grounded theory, we construct a system of driving factors comprising five primary indicators and eighteen secondary indicators. The hybrid model reveals the interrelationships, significance, system hierarchy, and dependence-driving relationships among these factors. Notably, the driving factor system is categorized into a six-level hierarchical structure, encompassing profound elements, such as policy optimization and digital empowerment, as well as surface-level factors, such as simplification of customs procedures and consumer demand forecasting. Based on the analysis results, this research proposes a set of pathways to achieve the sustainability of the supply chain. These strategies involve improving cross-border agricultural e-commerce policy frameworks, enhancing digital-driven supply-demand coordination, strengthening logistics infrastructure and transparency, and cultivating brand influence. The study's findings not only enrich the relevant theories but also provide practical guidance for the coordinated advancement of economic, social, environmental, and resilient development. Furthermore, they are conducive to advancing the United Nations Sustainable Development Goals.