Anaerobic digestion (AD) is considered a promising technology for the sustainable management of current large quantities of animal waste. However, the efficiency and underlying mechanisms remain poorly understood, particularly regarding the different characteristics of different types of animal wastes. The present study investigated the methane production, community structure, microbial viability, and enzymatic activity following mesophilic and thermophilic AD of four types of animal waste, including carnivores (lion), herbivores (elephant), and omnivores (hippopotamus and orangutan). Methane yield obtained with thermophilic AD of four animals was higher than mesophilic ones. The methane yields of lion manure under the mesophilic and thermophilic AD were 0.326 L/g VS and 0.391 L/g VS, respectively, higher than that of herbivore and omnivore waste. Bacteria were divided into low-DNA (LDNA) and high-DNA (HDNA) bacteria by flow cytometry based on DNA content. Compared with mesophilic AD, thermophilic AD had higher cells density, which has the same trend with methane production. The results showed that the live LDNA bacteria abundance was increased by 98.6% in orangutan manure AD system after heating up to 55 ℃. However, most of the dead bacteria were HDNA, indicating sensitivity of HDNA cells to environmental conditions. For functional enzymes, the activities of dehydrogenase, phosphotransacetylase and protease were enhanced in the thermophilic AD system of all kinds of animal manure. Nevertheless, the acetate kinase activities of herbivorous animal manure and coenzyme F420 activities of omnivorous animal manure had been inhibited at high temperatures.