Abstract: The physical effects of ultrasonic and microwave in salmon peptides had been studied. The structural changes of peptides were measured by ultraviolet-visible spectrophotometry and fourier transform infrared spectroscopy and the amino acid composition was also determined. The results showed that the superoxide radical scavenging capacity were all improved using ultrasonic, microwave and ultrasonic-microwave. The ultra-violet of the peptides treated by ultrasonic-microwave and microwave showed blueshifted (its peak shifts towards the blue end of the spectrum) , while ultrasound-induced unchanged. The positions and intensities of the infrared absorption peaks in 1669 cm-1 C=O and 1544cm-1 N-H were all changed. The secondary structure of salmon peptides had been changed treated by ultrasonic-microwave, microwave and ultrasound. The amino acid composition of peptides showed that antioxidative amino acids did not changed significantly. That's proved that its active substances were small molecular peptides.