In order to enhance the scientific understanding of the transition law of rural residential areas and enrich the theory and method system of land use transition research, this article takes Shandong Province as an example and constructs a comprehensive research framework of rural residential land scale, structure, and function from the perspective of the combination of the macro and micro scales based on differences between the rural residential areas in the region and the village scale forms. Using model quantitative analysis and horizontal comparative analysis methods, this paper explores the process characteristics of rural residential land use scale transition and the corresponding stage differentiation law of spatial structure and system function. Research has shown that the stage characteristics of the scale transition of rural residential land use in Shandong Province in the past 10 years are significant. The five transition stages—from the primary stage, low stage, intermediate stage, advanced stage, to the stable stage—show obvious spatial agglomeration and spatial autocorrelation, which are mainly driven by the positive and negative interactions of economic development, the policy environment, natural conditions, and population. With the gradual upgrading of the land use scale in rural residential areas, the spatial pattern of rural residential areas has been continuously optimized, the land use structure has tended to be balanced and complicated, and the living-production-ecological function as a whole has been strengthened. The essence of this type of differentiation is the differential performance of rural residential areas adapting their own conditions to the external environment. The transition of the rural residential area from the macro to the micro scale is also the process of realizing rural reconstruction and rural revitalization. In the future, under the framework of the “element–structure–function” system of rural residential areas, the rural transition and development should be continuously promoted through the support, organization, guidance, and promotion mechanisms of internal and external factors.