Polymer nanocomposites have been widely used in the preparation of coating agents in the leather industry. Considering the complex bio-effect and ecological risk of nanomaterial, research on the biodegradability and biocompatibility of polyacrylate/metal nanocomposites in activated sludge system is of specific significance. We investigated the change of the bacterial community and diversity of activated sludge fed with polyacrylate/ZnO nanocomposites in both low (500 mg COD /L) and high (1000 mg COD/L) doses. COD removal, dehydrogenase activity, and total protein of activated sludge system were monitored in all treatments over 30 days. The results demonstrated that the exposure to both polyacrylate/ ZnO nanocomposite and polyacrylate decreased the dehydrogenase activity at early stage comparing to the control, but had no significant influence on COD removal. Overall, the bacterial communities in activated sludge were resistant to polyacrylate/ZnO nanocomposites, and had higher levels of metabolic activity, protein accumulation and bioavailability when exposed to these chemicals comparing to the control especially at later stages of incubation (15–30 days), which indicated that these polyacrylate/ZnO nanocomposites of certain amount were biocompatible to activated sludge system.