Great attention has been paid to the toxicity effect of Zinc oxide nanoparticle (ZnO NPs) on wastewater anaerobic digestion, particularly the methanogenesis process. However, few research was done on how to reduce ZnO NPs toxicity on wastewater digestion. In this study, different dosages of granular activated carbon (GAC) were added into the wastewater digestion system exposure to ZnO NPs, and the inhibition of ZnO NPs on the methanogenesis was found to be significantly reduced. Compared with the 49.5% methane inhibition rate caused by 100 mg/g-TS of ZnO NPs, the methane productions were respectively increased by 15.6%, 50.0% and 92.8% while adding 10, 20 and 30 mg/L of GAC into the wastewater digestion system. The monitoring of volatile fatty acids (VFAs) variation shows the accumulation phenomenon of intermediate VFAs, which was resulted from the inhibited aceticlastic methanogenesis by ZnO NPs. However, the VFAs accumulation was no longer occurred in the wastewater digestion exposure to both ZnO NPs and GAC. It means that the addition of GAC improved the transformation of those VFAs to methane. Moreover, the pH was largely increased simultaneously. It was speculated that the reactive carbony group AC=C=O in GAC was dissociated to form OH-. Thereby, the accumulated organic acid was neutralized and the pH was increased. With the increasing pH, the dissolution of Zn2+ from ZnO NPs was slowed down and the biological toxicity of Zn2+ to methanogens was correspondingly reduced. Scanning electron microscopy analysis indicated that the adsorption of ZnO NPs to the surface of GAC probably reduced the effective contact of ZnO NPs to microorganisms, ultimately attenuating their toxicity. Another possible reason is that GAC promoted the direct electron transfer between syntrophobacter species and methanosaeta species, correspondingly improved the methanogenesis process.