, a rare freshwater shellfish with high protein quality, is unique to China. However, the poor hydrosolubility and functional properties of proteins hinder their utilization in food products. Herein, the alkaline dissolution-isoelectric precipitation method was used for the extraction of proteins. Furthermore, the impact of high-pressure homogenization (HPH) treatment varying from 0 to 100 MPa on the structure and functional properties of proteins was investigated. The obtained results indicated that HPH treatment decreased the α-helix content and enhanced the β-sheet and random coil content. Furthermore, the HPH caused the unfolding of protein structure, exposing aromatic amino acids, increasing the free thiol group content, and enhancing surface hydrophobicity. As the homogenization pressure increased from 0 to 100 MPa, the particle size of proteins decreased from 899 to 197 nm with the polymer dispersity index (PDI) value decreased from 0.418 to 0.151, the ζ-potential increased from -22.82 to -43.26 mV, and the solubility increased from 9.54% to 89.96%. Owing to the significant changes in protein structure and solubility, the emulsifying, foaming, and digestive properties of proteins have been significantly improved after treatment with HPH.