To control seafood quality and regulate oyster aquaculture in Qinzhou Harbor, Beibu Gulf, the oysters (Crassostrea rivularis) were collected from three stations in the region in 2015, and analyzed by atomic fluorescence spectrophotometer and atomic absorption spectrometer. Overall, the content of heavy metals in Crassostrea rivularis exhibited Zn>Cu>Cd>Cr>As>Pb>Hg, and contents of Zn and Cu had the average of 532.03 and 126.96 mg/kg, respectively. Referring to aquatic products standard of NY 5073-2006, we found, with the exception of Crassostrea rivularis collected at the 2nd station of July, the level of Cu from 89% samples exceeded the limit. While referring to aquatic products standard of GB 2762-2012, only the level of samples from the 3rd station of July went beyond the limit. Contents of Pb and Hg were low, with an average of 0.02 and 0.009 mg/kg, respectively. The dietary intakes of heavy metals in Qinzhou Harbor's Crassostrea rivularis were lower than the recommended values of Joint FAO Expert Committee on Food Additives (JECFA), thus the oysters in this region are safe for edibility.