This study aimed to realize the full processing and utilization of isolated protein from flaxseed meal. Flaxseed protein isolate and degummed and defatted flaxseed protein isolate (DD-FPI) were prepared from the cold-pressed flaxseed meal (FM) using ultrasound-assisted aqueous extraction. A comparison was also made on their physicochemical, structural and functional properties. The results showed that the protein mass fractions in the FM, and degummed and defatted flaxseed meal were (37.52 +/- 0.04) % and (37.47 +/- 0.02) %, respectively. The degumming and degreasing treatment of FM increased the protein purity by about 15% before protein extraction. The molecular weights of FPI and DD-FPI were determined to be 10-55 kDa, indicating the most outstanding protein bands. A total of 17 amino acids were identified in each of them, including the abundant essential and non-essential amino acids. FTIR spectroscopy showed that the secondary structures of FPI and DD-FPI were similarly the looser structure, withaverage stability. SEM observed that the FPI exhibited the lower microscopic porosity than DD-FPI. The XRD diffraction intensities and peak shapes showed that there was less crystallinity or orderly arrangement in the structures of both FPI and DD-FPI, where the crystallinity of DD-FPI was lower than that of FPI. The amphiphilicity, hydrophilicity and the lipophilicity of the two proteins were better than those of soybean protein isolate. Both FPI and DD-FPI presented the excellent alkali solubility at different pH and salt ion concentrations. The foaming ability, emulsification activity and emulsion stability of DD-FPI were better than those of FPI, while the foam stability was the opposite. Therefore, the two isolated proteins can be expected to apply into the field of functional food.