National-or regional-scale comprehensive geographical regionalization, including the designation of biogeographical regions, can provide foundational data designed to enhance the conservation of biodiversity and the construction of a nature reserve system and so provide a scientific basis for the establishment of policies related to local biodiversity. The comprehensive geographical regionalization supporting natural conservation has become an important aspect of the field of natural geographical regionalization with the development of nature reserves. Meanwhile, China's nature reserve system has been preliminarily established and is developing rapidly. However, no national geographical regionalization system is in place that designates biogeographical regions, considers both biotic factors (such as plant, animal, or vegetation) and abiotic factors (such as climate, soil, or landform), and is also designed to provide a basis for biodiversity conservation and the establishment of nature reserves. This study uses a geographic information system (GIS) to first divide the territory of China into 3489 basic geographical units based regional climate, soil and geomorphology. A regionalization of various aspects of biogeography such as climate, soil, flora, animal distribution, and vegetation was conducted for this study. Then, the spatial information used to create biogeographical regions was compiled and converted into attribute information that could be used to analyze the differences between all the basic geographical units using GIS10.0. Next, the entire set of data supporting these geographical units was studied using TWINSPAN and PC-ORD4.0. Finally, a natural conservation comprehensive geographical regionalization scheme designed to conserve and preserve natural resources was proposed based on the classification results; data from the vegetation regionalization and geomorphologic regionalization were included. Data analysis included quantitative and qualitative analysis during the course of the study. This comprehensive geographical regionalization system resulted in the designation of three major types of natural conservation biogeographical areas, including eight zones, 37 areas, and 117 subareas. A comprehensive geographical regionalization should consider an ideal combination of various elements of the landscape including soil, landform, climate, plants, animals and vegetation to support comprehensive natural area conservation, based on the zonal distribution of various ecological factors and eliminating the interference of intrazonal characteristics. Certainly, the boundaries of a comprehensive geographical regionalization system cannot be determined by the boundary of a single aspect of biogeography, and the biogeographical regions created here will be very different from other previous classification systems because this research integrates the expression of a wide variety of ecological factors in geographical space to consider the needs of biodiversity conservation and provides baseline information in support of the establishment of nature reserves. The features of the comprehensive geographical regionalization system include: (1) A geographical regionalization method that was based on the numerical taxonomic methods of TWINSPAN and GIS, used innovative technology and methods, and provides a new approach for research related to geographical regionalization; (2) Quantitative criteria that are proposed in combination with the existing special regionalization in this study; these criteria helped researchers avoid artifacts in the data that were based solely on one aspect of the data such as unique characteristics of the animal and plant indices, resulting in poor selection of biogeographically-based polygons; additionally, the quantitative criteria can comprehensively reflect natural ecological characteristics in a particular district and can provide good direction to land managers concerned with biodiversity conservation and nature reserve construction; (3) Quantitative analysis was used to ensure that the geographical regionalization system was constructed objectively, while qualitative analysis was used to avoid obvious errors and to improve the accuracy of the classification.