The coordinated development of territorial space is the premise of regional sustainable development. How to optimize the territorial space structure and build a reasonable control model has become one of the important issues that need to be urgently solved. This study took Wenshan city in Yunnan province, a typical karst mountainous area, as an example. It explored the optimization method of territorial space based on the "dual evaluations" and the amendment rules of conflict areas to optimize the territorial space partitions and propose control models for territorial space partitions and rocky desertification partitions. The results showed that: (1) The territorial space of karst mountainous areas in Yunnan province could be divided into 6 types, namely, urban development boundary area, urban reserved area, permanent basic farmland area, general agricultural area, ecological protection red line area, and general ecological area. Among them, the ecological protection red line area had the largest area, while the urban development boundary area had the smallest area. (2) The urban development boundary area and the urban reserved area were mainly distributed in the east and southeast; the permanent basic farmland area and the general agricultural area were mainly distributed in the north and south; the general ecological area was in the northwest and southwest; and the ecological protection red line area was in the west, south, east, and northeast, and the east and northeast parts of the study area were mainly rocky desertification areas. (3) According to the development potential and trend of each territorial space type, the control measures and models for territorial space partitions were proposed. For the areas of mild, moderate and severe rocky desertification, the paths and methods of development and protection in rocky desertification partitions were proposed for urban space, agricultural space, and ecological space. The results of this research can provide decision support for the reasonable development of territorial space and the control of rocky desertification in karst areas, and the methods and ideas of this research can provide references for territorial spatial optimization and control.