Abstract: GIS technology features convenient data management, powerful spatial analysis and intuitionistic 3D visualization capacities and its application in the harnessing of clean small watershed can effectively realizes massive data management, complex spatial analysis and decision making to provide the powerful support for beautiful countryside construction. Taking Caomiaogou small watershed in Xichuan County of Henan Province as a case, this paper gives a detailed presentation to the technological route of clean small watershed harnessing by GIS technology. By using GIS technology, the information on different-level water catchments, vegetation coverage and land types can be obtained from high resolution image. In the combination of the measured water quality data and investigation data of soil, pollution and rainfall etc. and with the technology guidance of clean small watershed demonstration projects as the standard, it is convenient to perform watershed division in the harnessing areas, 3D construction design, investment estimation and benefit analysis. The application of GIS technology can effectively improve the management level of clean small watershed.