The total amount of manure production increased fast in response to rapidly increasing demand for livestock production, which poses a strong public health threat due to the greenhouse gases (GHG) emissions and leachates without appropriate treatment. Anaerobic digestion is available technology for livestock manure treatment with new business opportunities and benefits for the society, such as bioenergy of CH4 and nutrients are extra income, odor and pathogens are reduced and GHG emission are limited. The productions of chicken manure, cattle manure and pig manure were introduced with evaluation of potential energy production. The toxicity of ammonia/ammonium in the anaerobic digestion process was evaluated with microbial community dynamics. Operation conditions effects on methane production were analyzed, such as pH, organic loading rate (OLR) effects and the ammonia stripping pretreatment effects on the CH4 conversion. The dynamic of functional archaeal and bacterial community were also conducted. Methanosaeta dominated in the steady stage of chicken manure thermophilic digestion but Methanothermobacter dominated in the inhibition stage and Methanosarcina thrived in the recovered stage. In contrast, under mesophilic conditions, Methanosarcina dominated in the steady stage while in the inhibition stage Methanosaeta and Methanoculleus thrived and lastly recovered to Methanosaeta. Poultry manure can be easily inhibited by ammonia compared to cattle manure and pig manure digestion since it has a high nitrogen content, which was more suitable for mesophilic digestion with evidence of process resilience in mesophilic digestion. Pre-treatment of ammonia stripping or co-digestion are the effective ways to generate a stable process.