Metabonomics profiling of Yunnan and Ethiopian coffee beans were conducted by UHPLC-QE-MS， to investigate the differences metabolites of green coffee beans in different regions of Yunnan Province and the characteristic components compared with those in Ethiopia. The results showed that there were 36 differential substances in Yunnan green coffee beans compared with Ethiopian green beans， including 16 metabolites of polyphenols such as 3-O-caffeoyl-1-O-methylquinic acid and epicatechin； 8 metabolites of lipids， such as octadecatrienoic acid； 6 metabolites of sugars， such as agnuside； and alkaloids， organic acids， terpenes. Among them， the contents of 24 compounds such as mammeigin， agnuside， 3-O-caffeoyl-1-O-methylquinic acid， 2，2-dimethylsuccinic acid and octadecatrienoic acid in Yunnan green coffee beans were significantly higher than those in Ethiopia green coffee beans， and 12 compounds such as epicatechin， cassitoroside and lipoxin in Ethiopia were significantly higher than those in Yunnan. The analysis of Yunnan green coffee from different regions showed that there were 44 differential metabolites， including 14 metabolites of amino acids such as glutamic acid and alanine； 11 metabolites of fatty acids such as palmitic amide and arachidic acid； 10 metabolites of polyphenols such as chlorogenic acid and quinic acid； malic acid and other 3 organic acids， and terpenoids， sugars， alcohols， others. The results showed that UHPLC-QE-MS combined with multivariate statistical analysis method could be used to study the differences of metabolites of coffee beans in different regions， providing theoretical basis for origin traceability of coffee beans.