The accelerated development of economic globalization has given rise to the formation of supply chain networks for cross-regional agricultural products. However, the unequal rights and status of the partners and an imperfect benefit linkage mechanism have made it difficult to reasonably distribute and share benefits. Understanding how to establish a benefit-sharing mechanism among partners has been a popular topic in the industry, but thematic research and discussions are lacking in the academic community. Therefore, in this study, we utilized a grounded theory approach and selected five supply chain master enterprises with different supply chain systems as samples. We constructed a theoretical model of a benefit-sharing mechanism and systematically revealed the key elements and theoretical logic of benefit sharing. The results of this study showed that (1) the five elements of benefit creation, benefit integration, benefit distribution, benefit constraint, and benefit coordination have important impacts on benefit sharing in the supply chain; (2) the dimensions within these five elements are independent of each other, and these elements can be combined to demonstrate a common impact on benefit sharing. The dynamic interaction among the five elements constituted a self-regulating and self-optimizing cyclic system; (3) benefit integration and benefit distribution have a dynamic cyclic facilitating effect on benefit sharing. This study has refined the key elements of the benefit-sharing mechanism, and the results provide theoretical references for benefit sharing and in-depth collaboration among supply chain members.