Greenhouse gas can lower livestock production. Manure management systems in Taiwan vary from the IPCC model for the Far East and Asia region. This study centers on three pig farms and dairy farms in northern, central, and southern Taiwan. Analyzed GHG samples from in situ anaerobic wastewater treatment systems of pig farms revealed emission factors of GHG were CH4 (1.39308855, 0.46201221, and 0.44907150 kg/head/yr), CO2 (1.27948507, 0.44290146, and 0.420810940 kg/head/yr), and N2O (0.00248757, 0.00113081, and 0.00135421 kg/head/yr) in three temperature periods (cool, temperate, and warm, respectively). Analysis results indicated that emissions factors of CH4 from pig farms were lower than those of IPCC (1996b) under both temperate and warm temperature periods. Analyzed GHG samples from in situ anaerobic wastewater treatment systems of dairy farms revealed CH4 emission from dairy farms were lower than those of IPCC (1996b).