Defatted krill powder, rich in protein, has emerged as a potential, novel food raw material. The present study aimed to prepare Antarctic krill protein from the supernatant (AKP-S) and precipitation (AKP-P) using the ultrasound-assisted alkali dissolution and acid precipitation method, and analyze their composition, structure, and functional properties were analyzed. The protein contents of AKP-P and AKP-S were more than 85% (dry weight), and their total amino acid content was 48.75 and 43.59 g/100 g of protein, respectively. The SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and surface morphology analysis (SEM) results showed that the AKP-S was degraded during acid treatment and had a smaller particle size than AKP-P. The α-helix and random curled structures of AKP-P and AKP-S were few or even disappeared. The solubility of AKP-S was more than 70% in the pH range of 3–13, and the change in AKP-P solubility with pH was consistent with the trend of β-sheets. Except for pH 7.0–9.0, the solubility of AKP-P and AKP-S with pH was positively correlated with surface-hydrophobicity (H₀). The emulsifying activity of AKP-P and AKP-S at different pH was approximately positively correlated with the solubility. The minimum gel-forming concentration of AKP-P was 8%, while AKP-S could not form gel at 14%. The gel water holding capacity reached more than 90% when the AKP-P concentration was 12%. The rheological results showed that the storage modulus (G′) predominated over the loss modulus (G″) of AKP-P in the range of 8%–14% concentration.