Objective: This study aimed to investigateing amino acid content and quality difference of different flaxseed varieties, based on their amino acid content. Methods: 12 flaxseed varieties from 6 producing areas were used to tested materials, amino acid contents in flaxseed were measured and 17 amino acid contents were used to assessing index, which was analyzed by principal component and clustering for studying the amino acid content and quality difference of flaxseed based on amino acid content. Results: affected order of flaxseed varieties on different amino acid content was Met>Cys>Phe>Tyr>Arg>Glu>Pro>His>Asp>Ser>Lys>Gly>Thr>Ala>Ile>Val>Leu. Three principal components were extracted, and their accumulative variance contribution rate reached 86.695%; Ala, Arg, Thr, Leu and Cys could be used as a comprehensive assessing index of 12 flaxseed varieties on amino acid content. The order of 12 flaxseed quality from good to bad based on amino acid content by subordinate function method was obtained, and the order was Jinya7>Jinya8>Lunxuan2>Baya9>Yiya3>Lunxuan1>Ningya16>Ningya17>Yiya4>Longya8>Baya11>Longxi10. Conclusion: Jinya7 is the best flaxseed variety, and Longya10 is the worst flaxseed variety in comprehensive quality; 12 flaxseed varieties were divided into four classes by comprehensive assessment.