This study aims to evaluate the carcinogenic risk of PAHs in the drinking water of counties along the Huai River in China and study their associations with high cancer incidence in local population. We investigated 20 villages with high cancer incidence rates as the risk group and 20 villages with low rates as the control group. Water samples from each village were collected in the winter and summer seasons to analyze the concentrations of 16 PAHs. The carcinogenic risks of the PAHs were calculated for each village using a health risk assessment approach. Results showed that PAHs concentrations in 27.2% of the water samples were higher than the allowable values in China. However, no significant difference in water PAHs concentrations was observed between the risk and control groups (P > 0.05), and no correlation was found between water PAHs concentrations and cancer incidence in these villages. The average upper bound carcinogenic risks were less than 1 × 10−4 in both groups. In conclusion, PAHs were present in the drinking water of the studied villages, but their carcinogenic risks remained within acceptable limits. PAHs in local drinking water might not be the major environmental cause of the high cancer incidences.