Flaxseed lignan macromolecules (FLM) are a class of important secondary metabolites in flaxseed, which have been widely concerned due to their biological and pharmacological properties, especially for their antioxidative activity. For the composition and structure of FLM, our results confirmed that ferulic acid glycoside (FerAG) was directly ester-linked with herbacetin diglucoside (HDG) or pinoresinol diglucoside (PDG), which might determine the beginning of FLM biosynthesis. Additionally, p-coumaric acid glycoside (CouAG) might determine the end of chain extension during FLM synthesis in flaxseed. FLM exhibited higher antioxidative activity in polar systems, as shown by its superior 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging capacity compared to the 2,2’-azinobis(3-ehtylbenzothiazolin-6-sulfnic acid) (ABTS) cation free radical scavenging capacity in non-polar systems. Moreover, the antioxidative activity of FLM was found to be highly dependent on its composition and structure. In particular, it was positively correlated with the number of phenolic hydroxyl groups (longer FLM chains) and inversely related to the steric hindrance at the ends (lower levels of FerAG and CouAG). These findings verified the potential application of FLM in non-polar systems, particularly in functional food emulsions.