Eco-sensitivity evaluation is the basis for land development and has practical significance to the establishment of environmentally-friendly economic and social development models. Compared to simple geomorphic regions, complex geomorphic regions are limited by a higher number of eco-sensitivity factors under a land exploitation context. Further still, these factors have complicated spatial characteristics and affect each other. Based on published data, we focused on the city of Qinzhou in Guangxi Zhuang Autonomous Region, China and developed an eco-sensitivity assessment system spanning land ecology, water ecology and plant ecology. A systematic comprehensive assessment of all watersheds was done using qualitative classification, spatial quantitative modeling, remote sensing and GIS technology. We were able to group Qinzhou's 273 watersheds into three types: high sensitivity areas, medium sensitivity areas and low sensitivity areas. We propose a limit on land exploitation activities in high sensitivity areas and an ecological security network. The methods utilized here can help determine eco-sensitivity characteristics in complex geomorphic regions and with this knowledge governments will be able to develop robust scientific policy to protect regional ecological security.