In order to tackle the problem of unsafe water quality in rural area, 81 water samples of rural drinking water source in Mingshan County are detected. The health risk model recommended by the U.S. National Research Council of National Academy of Science is used to calculate and analyze the water carcinogenic risk and the non-carcinogenic risk, then the spatial analysis of ArcGIS and proper interpolation methods are used to analyze the result of the assessment. Spatial distribution maps of water quality risk are drawn, and the single factor and the multi  factor of the health risk of carcinogens and non-carcinogens of the water quality are assessed. Research results show that the main carcinogens in water source area are As, Cr and Pb, and the main non-carcinogenic risk comes from arsenic, fluorides, nitrate, and ferrum. This study reveals the control index of the health risk of the water source in the studied area and provides scientific basis for the treatment of the water source areas.