We presented a comprehensive groundwater quality assessment based on Fuzzy-Grey model in Qinghai Province, China. The results showed that the groundwater quality of Golmud was better and in grade II,and that of Xingning and Haidong Prefecture was both in grade III. The specific order of groundwater quality in three different region was Golmud >Xining> Haidong Prefecture, which was the same as Standard Recommendation and also indicated that the Fuzzy-Grey comprehensive method was practicable and feasible. Meanwhile, we used the National Academy of Science’s RA framework as a guide, to analyze the groundwater health risk in this area. We found that personal average annual total risk exceeded the acceptable level of risk, among which the maximum at the cost of 1.99×10-4 a-1 appeared in Golmud, which was about four times of standard ICRP recommendation, and two times and four times for Xingning and Haidong Prefecture, respectively. The sequence of total risk was Golmud >Xining> Haidong Prefecture in these three regions, and the Hexavalent chromium was the main contributor to the total risk. This study could provide a scientific basis for local groundwater exploitation and risk management through the groundwater quality evaluation and health risk analysis.