The effects of various dosages of graphene oxide (GO) on the performance of anammox and the underlying mechanisms are not yet fully understood, necessitating the provision of additional details. In this work, the dosage-dependent impacts of GO on the anammox system were investigated from the perspective of molecular biology analysis. The nitrogen removal efficiency (NRE) continuously increased at 10−100 mg/L GO, and a high nitrogen removal rate (NRR) was obtained at 25 mg/L GO. GO also improved the content of extracellular polymer substance (EPS) and the abundances of hzs and nirS genes. Molecular docking demonstrated that GO had a strong binding with the hydrazine synthase enzyme. Microbial analysis revealed that denitrifying bacteria, such as Denitratisoma and OLB13, were enriched, indicating that the high NRE could be attributed to the synergistic effect between denitrification and anammox processes. The analysis of microbial functions suggested that GO could impact various metabolic activities, such as quorum sensing, extracellular electron transfer, and membrane transport. Above all, this work provided detailed insights into the effects of different GO dosages on the anammox system.