Antibiotic contamination in drinking water sources has been increasingly prominent in recent years. The water quality in the Chongqing area is not only essential for the local people but also is crucial for the downstream of Yangzi River. To understand the level of antibiotic contamination in the large-scale drinking water sources, this study measured antibiotic residues in nine large-scale drinking water sources (five urban drinking water sources and four township drinking water sources) in Chongqing area of the Yangtze River. Results demonstrated that eight antibiotics of three categories in total were detected, including sulfonamide metformin (SMX), sulfonamide metformin (SMZ), erythromycin (ERM), Roxithromycin (ROM), Tylosin (TYL), Lincomycin (LIN), Chloramphenicol (CAP), and Florfenicol (FF). The mass concentration of antibiotic residues in five urban drinking water sources ranged from 13.9 to 76.6 ng/L, with an average of 46.4 ng/L, and that in four township drinking water sources ranged from 20.6 to 188.1 ng/L, with an average of 88.45 ng/L. The mass concentrations of antibiotic residues in Chongqing area were much lower than those in other cities. Antibiotics posed the maximum risk with a value of 0.005 for 0–3 months of the infant. The risk quotients of antibiotic residues in all water sources were much lower than 1 and thus did not pose a direct threat to human health.