Agricultural land transfer is one of the basic conditions to realize agricultural modernization. In the process of the central government promoting the reform of the land system, local innovations in the agricultural land transfer system have continuously emerged, showing significant practical differences. A deep exploration of the practical differences in the agricultural land transfer system helps to fully understand China’s agricultural land transfer system and its innovation path. However, most existing studies are based on the theory of institutional change in institutional economics, ignoring the social environment in which the agricultural land transfer system is formed, especially the social basis and political process of the agricultural land transfer system, and also lack an explanation for the logic of the generation of regional differences in the agricultural land transfer system. Based on the perspective of “regional differences between the east and the west”, this paper constructs the analysis framework of the “functional attribute-governance structure” of the agricultural land transfer system. Taking Z County in Southern Jiangsu Province and S County in Hubei Province as the case study, this paper discusses the differences and practical logic of the agricultural land transfer system in different regions. The study finds that the differences in the level of rural industrialization and the capacity of grassroots governance lead to the differences in the agricultural land transfer system between the two places. In Z County of Suzhou, the highly developed rural industrialization accelerates the non-agricultural transfer of labor, strengthening the economic attributes of the agricultural land transfer system; the good economic conditions also provide the grassroots with sufficient governance resources, forming a governance pattern of agricultural land transfer with joint governance by the government and society. In S County of Hubei, the de-industrialized countryside cannot provide sufficient employment opportunities, and the agricultural land transfer system still has welfare attributes; the weak economic foundation also leads to a lack of grassroots governance resources, and agricultural land transfer is spontaneously carried out within the community, forming a governance pattern of agricultural land transfer based on relational governance. Compared with existing literature, this paper makes the following two extensions: First, by comparing two typical cases, it presents the differences in the agricultural land transfer system in different regions and explains the regional differences in the agricultural land transfer system from two dimensions: functional attributes and governance structure. On this basis, this paper proposes that the difference in the agricultural land transfer system between Z County in Suzhou and S County in Hubei is essentially a product of the east-west economic differences. Second, by presenting the differences in the agricultural land transfer system, it explores the feasible path of agricultural land transfer system innovation, providing enlightenment for further improving the land system and comprehensively deepening reforms. In the eastern developed areas, the key to the innovation of the agricultural land transfer system is to improve the efficiency of agricultural land resource allocation while further preventing market risks. In the central and western regions, the key to the innovation of the agricultural land transfer system is to give full play to the coordinating role of the village collective, while reasonably using the resources of the rural society and effectively protecting the land rights of farmers. This study presents the regional differences in China’s agricultural land transfer system to some extent and explains the logic of the generation of these regional differences, which helps the country to promote the innovation of the agricultural land transfer system and improve and develop the socialist system with Chinese characteristics on the basis of fully respecting regional differences.