The spatial organization law of territorial function-structure is the basic theoretical problem of human-earth system coupling research, as well as the basic theory of carrying out territorial spatial planning and shaping sustainable geographical pattern. Starting from the discussion of geography on the repetition, prediction, regulation and optimization of geographical processes, this paper explains that the spatial governance system is an important way for modern geography to regulate and optimize the sustainable geographical processes and patterns. The spatial and temporal evolution characteristics of the spatial structure of territorial function composed of ecological-life-production (also known as three living spaces) are adopted to express the spatial order law of territorial function - structure, and explain some spatial organization goals, e.g., the coordination between territorial function and natural geographical environment, the minimization of various functions and conflicts between different units in the same region, the effective transmission of territorial functions in different spatial scales, and the maximization of comprehensive benefits in a long time scale. On the one hand, from the perspective of sustainability, the concept of four attributes of natural elements -- resources, environment, ecology and disasters -- is proposed. Through the integration of the four attributes, the natural carrying capacity is constructed, and the function of the original value, remaining value and potential value of carrying capacity in spatial planning is analyzed, so as to form the basic method of analyzing spatial organization from bottom to top. On the other hand, starting from new spatial equilibrium, the basic method of top-down spatial organization analysis is formed based on the territorial functional suitability of carrying capacity, integrated position and spatial structure parameters. Furthermore, the basic and strategic values of the major function zoning formed by the two methods for spatial organization and planning are discussed, and a new idea of separation and interrelation of the zoning, strategy, system with planning of utilization is proposed. With the implementation of the strategy of major function zoning as the main line, the spatial scale-down conduction of major functions as the core scientific problem, and the key constraint parameters as the control indicators of spatial structure, this paper discusses the database and territorial function pedigree, functional and scale-dependent carrying capacity evaluation method and model, and the construction framework of "Three Zones and Three Lines" (Three Zones represent ecological space, agricultural space, and urban space; Three Lines represent ecological conservation redline, permanent capital farmland, and urban development boundary), and demonstrates the way to implement the strategy of major function zoning in spatial planning. Finally, the paper puts forward some suggestions that geography should strengthen the construction of scientific and technological support system, e.g., the basic theory, method and technology of large and medium spatial scale (regional) territorial spatial planning.