Objective: It provides a basis for promoting the high-value utilization of flaxseed and its processing by-products in Qinghai. Methods: Using linseeds from different producing areas and varieties in Qinghai province as raw materials, and the content of lignan and its component-secoisolariciresinol diglucoside and secoisolariciresinol in 20 kinds of flaxseeds in Qinghai were determined by reversed-phase high performance liquid chromatography, based on DPPH and ABTS free radical scavenging ability to evaluate the antioxidant activity of these two lignans. Results: The content of lignans in flaxseeds from different producing areas and varieties in Qinghai Province was significantly different （P<0.05）, and the content ranges of secoisolariciresinol diglucoside and secoisolariciresinol were 7.53～23.33 mg/g, 0.85～2.55 mg/g, respectively. Secoisolariciresinol diglucoside and secoisolariciresinol have scavenging effects on DPPH and ABTS free radicals. There were significant differences in the antioxidant activity of lignans in 20 kinds of flaxseeds （P<0.05）. Conclusion: Linseeds from different producing areas and varieties in Qinghai Province have different lignan content, which has good antioxidant capacity.