This study aimed to comparatively elucidate the composition structure and techno-functionality of flaxseed protein isolate (FPI), globulin (FG), and albumin (FA) fractions. The results showed that FA possessed smaller particle dimensions and superior protein solubility compared to that of FG (p < 0.05) due to the lower molecular weight and hydrophobicity. FA and FG manifested lamellar structure and nearly spherical morphology, respectively, whereas FPI exhibited small lamellar strip structure packed by the blurring spheres. The Far-UV CD, FTIR spectrum, and intrinsic fluorescence confirmed more flexible conformation of FA than that of FG, followed by FPI. The preferential retention of free phenolic acids was observed for FA, leading to excellent antioxidant activities compared with that of FG in FPI (p < 0.05). FA contributed to the foaming properties of FPI, relying on the earlier interfacial adsorption and higher viscoelastic properties. FA displayed favorable emulsifying capacity but inferior stability due to the limited interfacial adsorption and deformation, as well as loose/porous interface. By comparison, an interlayer anchoring but no direct interface coating was observed for lipid droplets constructed by FG, thereby leading to preferable emulsion stability. However, FPI produced lipid droplets with dense interface owing to the effective migration of FA and FG from bulk phase, concomitant with the easy flocculation and coalescence. Thus, the techno-functionality of flaxseed protein could be tailed by modulating the retention of albumin fraction and specific phenolic acids.