Abstract: Tracing the evolution of the natural geographical pattern over the past thousand years by historical logic can better support policy recommendations for the future development of China’s territory condensed by administrative logic. We reviewed a large number of literature and summarized the unique natural environmental foundations and historical evolution laws of each region and zone, in order to propose policy recommendations for national spatial planning by historical, scientific, and administrative logic. We found that the modern geographical pattern of China has been formed by the billions years of evolution over geological period and ten thousand years of human activities over historical period. Under the influence of geological structures, monsoon movements, and river shaping during geological period, China’s land has differentiated into 3 natural regions (Eastern Monsoon Region, Northwest Arid−semiarid Region, Tibetan Plateau) and 2 transition zones (Farming−pastoral Zone, Coastal Zone). In historical period, humans have formed distinct production and lifestyle patterns tailored to local conditions, continuously transforming the spatial structure of the country, and thus forming each region’s and zone’s unique regional evolutionary histories. And we provided a detailed explanation and summary of the evolution process and laws in each region and zone, thus proposing suggestions for the national territory developing and protecting, such as following the natural ecological restriction and historical development law, maintaining the reasonable combination and material−energy exchange between natural and human ecosystem, and optimizing spatial pattern in transition zones.