As China’s rapid development has gradually expanded beyond urban areas, vernacular landscape as a significant expression of local conditions receives more and more attention. This paper aims to formulate a comprehensive zoning scheme for vernacular landscapes of China. The zoning applies zoning methods and technical means of the Geographic Information System. Based on the understanding of the vernacular landscape concept, the main factors that determine the feature of the vernacular landscape are identified, including landforms, climate, hydrology, vegetation, land use, settlements, housing, population, economy, and customs. Then, the indicators that can significantly reflect the characteristics of each factor are selected to construct an indicator system for comprehensive zoning. We combine quantitative and qualitative analysis to examine the spatial differentiation patterns of Chinese vernacular landscapes comprehensively. The prior zoning principle is a combination of the principles of relative consistency of natural constituents of vernacular landscape and relative consistency of human constituents of vernacular landscape. Simultaneously, it considers the combination of the principles of synthesis and dominant factors, the combination of the principles of top-down and bottom-up, the combination of the principles of spatial integrity and continuity, and the principle of hierarchical zoning. Based on indicator evaluation and essential zoning basis, using overlay analysis and comparative analysis methods, the country is divided into two-grade spatial units of vernacular landscapes by two steps: 8 vernacular landscape regions and 56 vernacular landscape sub-regions. It provides theoretical support for protecting and developing vernacular landscape characteristics, and exerting regional advantages to achieve comprehensive development.