Hydrological management of the Three Gorges Dam has resulted in the interception of heavy metals in the Three Gorges Reservoir (TGR). However, the exposure to heavy metals and health risks among local residents remained poorly understood. Here we collected 208 biomarker samples (hair) and 20 food species from typical regions in the TGR to assess the exposure levels of three toxic metals (Cr, Pb and As) in residents of the TGR, and subsequently investigated their health risk via dietary intake. Results indicated that hair Cr and As levels were below the reference value for normal people and threshold of skin lesions, respectively, whereas about 22% hair Pb exceeded the reference for clinical medicine, indicating a potential Pb exposure of local residents. Smoking habit and fish consumption were found to be predictors for hair Pb. In addition, the concentrations of heavy metals in all investigated food samples were below the limits of contaminants in food in China, except for Pb in the sweet potato and fish. The estimated daily intake of metals (DIMs) revealed that the intakes of Cr and As from studied food were under the recommended thresholds of Cr and As. However, the intake of Pb via diet exceeded the limit of the prevalence of chronic kidney disease and closed to the threshold for cardiovascular, which was probably associated with the high Pb concentrations of fish and sweet potato. Overall, residents around the TGR were at low exposure to Cr and As, but Pb exposure may need more attention.