Thermophilic anaerobic digestion, operated at a high temperature of 550C compared with other treatment processes, offers higher methane production, faster waste degradation, and better pathogen and virus reduction. It was widely used in treating sewage and animal wastes during the past decade. Ammonia is a common hydrolysis product during waste degradation and could cause inhibition when present in high concentrations. This study was conducted to reveal the effect of ammonia inhibition by focusing on methanogenesis, the most susceptible phase in anaerobic digestion. Besides, pH effect was considered, because pH could be an inhibition factor alone and interacts with ammonia inhibition by changing the relative ratio of ammonium to ammonia. Biomass exposed to different concentrations of total ammonia nitrogen (TAN) was used to study the acclimation effect. The response of these microorganisms was examined under inhibitory levels of TAN. In the later part of this study, models for ammonia inhibition and pH effect were assessed.