The increased endogenous synthesis and oil phase migration of main phenolic compounds in flaxseed were particularly important to the improvement of oxidation stability for flaxseed oil and the bioavailability for α-linolenic acid. The effects of appropriate germination (25℃, 24h) coupled with microwave treatment (700W, 1-5min) on the yield, color, lipid profiles, crystallizing and melting properties, antioxidant activity and oxidative stability of pressed flaxseed oil were investigated, and the release and migration of lignans and free phenolic acids into oil phase were studied. The results showed that the yield of pressed flaxseed oil decreased by 7.39% after 24h germination treatment (P<0.05), but consistently increased by 29.31% after microwave treatment for 1-5min (P<0.05), owing to the destruction of structural integrity of oil bodies and subsequent spillover and fusion, as well as extracellular leakage of lipid. When microwave treatment time extended from 1 to 5min, the ratio of C18∶3ω3 in LnLnLn evidently increased, which was accompanied by the ascending content of total phospholipids, as well as the ratios of phosphatidylethanolamine, phosphatidylglyceride and phosphatidylinositol in flaxseed oil (P<0.05). However, the microwave treatment had no obvious effect on the crystallization behavior and melting properties of pressed flaxseed oil. Moreover, compared with the untreated group, microwave treatment of flaxseed for 5min evidently reduced the contents of primary and secondary oxidation products, and simultaneously improved the oxidation stability and antioxidant activity of pressed flaxseed oil (P<0.05). These changes were mainly attributed to the oil phase migration of lignan macromolecules and its depolymerization product secoisolariciresinol diglucoside, as well as the free phenolic acid vanillin, vanillic acid and ferulic acid. This study aimed to elucidate the effect of germinating combined with microwave pretreatment on the quality characteristics of flaxseed oil, and provide a theoretical basis for the upgrading preparation of flaxseed oil and the high-value utilization of flaxseed.