Morphological changes of bacteria，E.coli，S.aureus，A.hydrophila，treated with antimicrobial peptide were observed by scanning electron microscopy. The results showed that the cells deformed severely，the surface of bacteria became rough and rumply，and the cytomembrane was ruptured after treated by antimicrobial peptide from intestine of grass carp. Moreover，research on its physicochemical properties showed antimicrobial peptide from the intestine of grass carp had an excellent thermal stability and strong resistance to trypsin activity.