Carbon-based materials are promising in improving the performance and stability of anaerobic digestion (AD). However, it is not clear if carbon-based materials would have any interaction with ammonia on AD performance, especially when ammonia is above inhibition level. This study aims to explore the effects of ammonia on carbon nanotube assisted AD reactors. Methanogenic performance, intracellular energy production, potassium transport activity as well as extracellular polymeric substance (EPS) changes were investigated. The results show that the presence of CNT may mitigate or worsen the ammonia inhibition depending on the total ammonia nitrogen (TAN) concentration. Further investigation found that potassium transportation process of the culture was disturbed with the presence of CNT, which dispatched the proton motive force. As a result, the intracellular energy level reduced, and the microbial detoxification capability decreased. TAN exhibited a strong positive correlation with microbes' detoxification activity, and CNT concentration was positively correlated with polysaccharide which created a physical structure to protect cell membrane.