Abstract: The content of flue-cured tobacco C3F amino acids in 18 counties of Henan province was classified research.Principal component analysis and hierarchical clustering method were used to analyze amino acids content in different regions.Main component analysis results showed that neutral amino acids，such as Phe，Gly and Ser，have a relatively large impact on study of 17 amino acids of flue-cured tobacco.When Euclidean distance is 3.03，18 counties of Henan province were divided into 4 categories.Establishment of an appropriate system of principal component analysis and hierarchical clustering model is more meaningful for study of amino acid content of different flue-cured tobacco-growing areas in Henan.