In order to explore the combined toxicity of carbon nanomaterial graphene oxide (GO) and perfluorooctane sulfonate (PFOS) in freshwater benthic shellfish, Corbicula fluminea was used as the target organism to study the effects of single and co-exposures of 1 mg/L GO or/and 500 ng/L PFOS for 28 days on body length, body weight, filtration rate, level of reactive oxygen species (ROS), antioxidant enzyme system and malondialdehyde (MDA) content. The toxicity was evaluated by enhanced integrated biomarker response (EIBR). The results showed that the body length and body weight of C. fluminea did not change significantly after exposure. Compared with the blank control and solvent control groups, the filtration rates in the single and co-exposure groups significantly decreased. Both GO and PFOS stresses significantly changed the enzyme responses in gills and visceral masses of C. fluminea with consistent variation trends in both organs. The EIBR results showed that the toxicity in gills and visceral masses of the co-exposure group was stronger than that of the PFOS or GO single exposure groups.