Flax (Linum usitatissimum L.) is an important oil crop in the high-altitude arid regions of China. Flaxseed is rich in various nutrients. However, the nutritional qualities of flaxseeds from different producing areas are still unclear. In this study, the nutritional characteristics of flaxseed from five producing areas in China were investigated. Twenty five nutritional quality indices in flaxseed were analyzed. Subsequently, chemometric methods, including cluster analysis, principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA), were employed to discover the characteristics of nutritional qualities in flaxseeds. The results revealed there are significant differences in nutritional qualities among flaxseeds from different production areas. Six quality indices including gamma-tocopherol, vitamin E, phytosterols, oleic acid, alpha-linolenic acid, and cycloartenol were susceptible to producing area. In detail, the superiorcharacteristic nutrients of Ningxia flaxseed, Inner Mongolia flaxseed and Hebei flaxseed are vitamin E (17.3 mg/100g), alpha-linolenic acid (52.6%) and cycloartenol (1738.1 mg/kg), and phytosterols (3032.0 mg/kg), respectively. This study promotes the high-value development and utilization of local flaxseed industry.