The Zhulin area of Yunnan is located in the watershed area of the Qingshuijiang river, Pumeihe river and Xiyangjiang river, tributaries of the Nanpanjiang river water system, with elevations 1,200 m to 1,960 m above sea level. Its geomorphology is dominated by peak cluster-depressions, karst valleys and karst hill-depressions. The karst is obviously stratified in vertical direction. Due to the extremely heterogeneous distribution and big burial depths of karst water in watersheds, it is a challenge to drill successful wells in this area. Based on the experiences of drilling at 9 wells from 1996 to 2012 in this area, this paper summarized the work processes for well drilling in karst watershed areas. It is suggested that in watersheds with weak runoffs, the targets should be chosen at the upper ends of large karst depressions on paleo-karst platforms close to watershed zones. In gentle slope zones with relatively strong runoffs, the effort should focus on the perched karst water above the suspension weak permeable layer which has relatively large area and gentle occurrence. In steep slope areas, groundwater in karst windows and shafts are the priority. Determining the locations of wells should follow such procedures as, first regional hydrogeological survey and then detailed hydrogeological investigations around well locations, with aid of some geophysical prospecting to improve the ratio of well drilling success. The wells to be drilled should not be located at discharge areas, strong runoff zones, or peak cluster-depressions, neighboring areas of big karst springs and groundwater flow, or bottoms of the negative landforms. The application of geophysical prospecting results should be closely combined with the results of hydrogeological surveys.