Ecological shelter zones reconstruction is an ecosystem restoration and conservation project aimed to the ecological safety of nations, regions and basins. Reconstruction of ecological shelter zones of the upper reaches of the Yangtze River became one of the most important tasks of Western Development strategy. This article, taking Zhaotong as an example, studies the functional regionalization of ecological shelter zones. The study supplies a case for functional regionalization of small and medium regions whose main tasks are environment reservation. With the guidance of theories of functional regionalization, and based on the analysis of Zhaotongs natural, ecological and socioeconomic factors, the paper suggests five principles for factors selection. These principles include: (1) reversing order evaluation; (2) selecting main factors; (3) keeping the integrality of administrative regions of towns; and (4) making the products acceptable by local government. To analyze spatial status of selected factors, LUCC data in 2002,1:50,000 relief maps and town-unit socioeconomic statistical data in 2004 are used. RS and GIS tools are also applied to melt traditional and modern geographical methods. This would be useful to functional regionalization research in mountainous areas. As a conclusion, the leading functional regions of ecological conservation or economic development are suggested, respectively. Zhaotong city is divided into two-level functional regions. The first-level includes three leading functional regions and they will lead developing direction of sub-regions. The second-level includes eight sub-regions, which are policy implemented regions, and will supply guidance to Zhaotongs ecological shelter zones reconstruction.