The effects of different extraction process on the protein composition and α-amylase inhibitory activity of seabuckthorn are systematically studied. There are five kinds of process for extracting seabuckthorn protein by using water, salt, alkali soluble acid, alcohol extraction combined with alkali soluble acid and alkali soluble acid combined with alcohol extraction respectively. The protein content, protein extraction rate, color, α-amylase inhibitory activity, amino acid composition and heavy metal content of seabuckthorn are compared and the optimal extraction process of seabuckthorn protein is determined. The results show that alcohol extraction combined with alkali soluble acid is the best process, and seabuckthorn protein content is (77.86±2.34)%, protein extraction rate is (73.18±1.8)%, amino acid composition is completely, α-amylase inhibitory activity can reach 85% for seabuckthorn protein at 1 mg/mL, and heat treatment at 80 ℃ does not affect the inhibitory activity. The detection results of heavy metal content show that the heavy metal content in the protein is lower than the national safety standard and could be used in food industry. This study has provided a theoretical basis for further processing and utilization of seabuckthorn protein.