The berries of Lycium barbarum L. (Goji) are widely used as a Chinese traditional herbal medicine and functional food because of their reported beneficial pharmacological effects. However, there are reports of Goji berries being contaminated by chemical residues that could pose a hazard to humans. In this study, samples of L. barbarum L. berries were collected from plantations in a genuine production area and supermarkets in Ningxia, China. The major hazardous chemicals, including pesticides (dichlorvos, omethoate, cypermethrin, fenvalerate, malathion, and deltamethrin) and metals (lead (Pb), cadmium (Cd), copper (Cu), nickel (Ni), zinc (Zn), and arsenic (As)), were quantified by gas chromatography and inductively coupled plasma-optical emission spectrometry. In addition, associated daily exposures and health risks were determined using deterministic and probabilistic assessments. The levels of five pesticides from the plantation samples were considerably lower than the maximum residue limits; only dichlorvos was detected in the supermarket samples, and deltamethrin was not detected in any samples. Cu, Zn, As, Pb, Ni and Cd were detected in samples from both sources. The hazard quotient values of individual hazardous chemicals and the hazard index of combined hazardous chemicals were considerably less than 1, indicating the absence of a non-carcinogenic effect of hazardous chemical exposures through Goji berry consumption. The R value of As was much less than 10^–6, which shows that consumption of the Goji berries had no obvious carcinogenic risks. The potentially harmful effects of the L. barbarum L. are more likely from berries obtained from plantations than those from supermarkets, and metal exposure is more dangerous than pesticide exposure. However, on the basis of our analysis, no population would be exposed hazardous chemicals exceeding existing standards, and the factors most affecting the health risk were exposure frequency and As content.