The preparation process of protein enzymolysis technology for the three-spot seahorse (Hippocampus trimaculatus Leach) degreased bone meal was developed. Two enzymes with better enzymolysis effect were selected from the five proteases, and the optimization condition of the Alkaline Protease is temperature – 54.7°C, pH – 9, duration of 6 h, the acquired rate of polypeptides was 11.77%; and that of Trypsin is temperature – 45°C, pH – 8.8, and duration of 4 h, and the rate was 11.49% by Response Surface Methodology. The strategy of compound enzymes was “Trypsin + Alkaline Protease”. The selected preparation process of active polypeptides by the compound enzymolysis technology acquired rate of polypeptides was 14.41 ± 0.16%, increased about 3% of acquired rate of polypeptides and 2.6–4.5% of the free radical scavenging rate than those of the single enzyme. The increased antioxidant capacity mainly came from the increased concentration of polypeptide in II^# peak, which increased about 10% of the free radical scavenging rate. The strategy of selected compound enzymes can effectively improve the utilization rate of seahorse protein.