In this work, we have presented a new method for species origin verification of collagen peptides based on DNA techniques. First, we investigate the changes in DNA during the preparation of collagen peptides including the total amount of collagen peptide DNA and the DNA degradation under different processing conditions. Secondly, we discussed the possibility of using polymerase chain reaction (PCR) for follow-up detection of collagen peptides. The results showed that the total amount of DNA decreased as the treatment intensity increased. The size of the cleaved fragments of DNA are mainly concentrated between 200 and 500 bp. On this basis, the combined PCR results finally determined that trace collagen peptide DNA can be effectively amplified with amplicons of about 300 bp to complete the verification of the species origin of collagen peptide. This study provides a new strategy for determining the authenticity of food labels for bovine collagen peptides.