The general status of the water resources in Yunnan Province and existing problems are analyzed in this paper. A DEM based on a 30 m resolution was use to extract the dam area and the watershed boundary, and superposition of the depth of surface runoff and groundwater runoff modulus data was conducted, in order to calculate the water resources supply in six different geomorphological areas in Yunnan Province. Safeguard measures for water resources capacity during the construction of towns that are built into the mountains of Yunnan Province are put forward, with consideration of rational and effective utilization of water resources, inter-regional and inter-departmental coordination, water infrastructure construction, and environmental protection.