Objective： To study the difference of comprehensive nutrition quality, different flaxseed varieties were investigated. Methods: 12 flaxseed varieties from 6 producing areas were used as research objects, eight nutrition components, including alpha-linolenic acid, were used evaluation index, 12 flaxseed varieties were evaluated by subordinate function methods and principal component analysis classified by clustering methodology. Results: Three principal components were extracted from 8 indexes by principal component analysis, and their cumulative contribution rate reaches 87.608%, reflecting better the comprehensive information of 12 flaxseed varieties. Crude protein, total amino acid, iron, and alpha-linolenic acid contents can be a comprehensive evaluation index of 12 flaxseed varieties by comprehensive analysis. Subordinate function methods assessed the quality of 12 flaxseed varieties. Twelve flaxseed varieties were clustered into four groups by clustering analysis, and their nutrition quality reduces in sequence. Group I includes Jinya8 and Baya11, and Group Ⅱ includes Jinya7, Baya9 and Lunxuan2; Group Ⅲ includes Lunxuan1, Yiya4, Ningya17 and Ningya16, and Group Ⅳ includes Yiya3, Longya8 and Longya10. Conclusion: Jinya7 is the best variety and Longya10 is the worst variety in comprehensive nutrition quality; flaxseed varieties were divided into four groups by comprehensive assessment.