Perchlorate and chlorate are ubiquitous pollutants in various types of foodstuffs, drinking water and environmental compartments. They have raised great concerns due to potential adverse effects on human thyroid functions. Dietary intake is considered as the predominant pathway for human exposure to perchlorate and chlorate. Nevertheless, data on human exposure to the chemicals above remain limited, particularly for the most vulnerable populations such as infants. In the present study, 62 breast milks, 53 infant formulas, 88 baby supplementary food and 50 tap water samples were collected in South China and the levels of perchlorate and chlorate were measured in these samples. Perchlorate and chlorate were frequently detected in more than 90% of measured samples. In these different types of samples, the median concentrations of perchlorate were 0.65 μg/L, 0.61 μg/kg, 0.56 μg/kg and 1.18 μg/L, respectively, while the median concentrations of chlorate were 1.73 μg/L, 2.48 μg/kg, 2.67 μg/kg and non-detected, respectively. Health risk assessment using hazard quotient suggested that perchlorate and chlorate exposure in the sampled baby food are not expected to increase the risk of an adverse health effect. To our knowledge, this is the first study simultaneously investigating perchlorate and chlorate exposure in Chinese infants via food intake.