Objective To understand the status and trends of drinking water quality in rural areas of Huaihe river basin. Methods According to the "prevention and control plan of cancer in Huaihe River Basin", we detected the drinking water in the Huaihe River Basin from 2011 to 2015. Results 1512 samples were detected in the five years. 978 samples exceeded standards, with exceeding standard rate 64.68%. The rate of decentralized water supply were significantly higher than that of centralized water supply (χ²=79.46, P<0.0001), and the exceeding rate of water quality in wet season was significantly higher than that in dry season (χ²=26.68, P<0.0001). In the decentralized water, the highest exceeding index was microbial index (35.98%), but in the centralized water the highest exceeding index was toxicological index(28.50%). The highest exceeded rate index was the fluoride exceeded index(24.80%) in the single index, followed by the total coliform group index(21.03%) and the total number of heat resistant colon index (19.05%), respectively. Conclusion The main risk factors affecting the quality of drinking water in rural areas of Huaihe River basin were high fluoride and microbial contamination.