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China is the country with largest livestock population in the world and the animal population increased rapidly. With the increase of animal population, the management systems have changed from extensive to intensive. Increased amount manure was managed under anaerobic condition, which can promote CH4 production. This study estimated CH4 emissions from AMMs in 1990 and 2000 using modified methods. Modifications on feed intake, swine manure management system usage (MS%), methane conversion factors (MCFs) for slurry and pit (storage period>1 month) manure management system at different climate conditions were made. CH4 emissions from AMMs in China from 1990 to 2000 by provinces were estimated using IPCC methodologies/data and modified methodologies. Total CH4 emissions from animal manure management systems were estimated to be 1550.0 and 2031.1 Gg CH4 in 1990 and 2000, respectively. It increased by 31.0% during this period. Swine was the largest contributor to CH4 emissions, while pit and slurry manure management systems had the largest share to CH4 emissions from AMMs.