The degradation characteristics of chitosan and biguanide benzoyl chitosan in hydrogen peroxide were researched in simple homogeneous system. The change of molecular weights of chitosan and biguanide benzoyl chitosan was measured in degradation procedure by gel permeation chromatography method.The change of the glycan substitution degree of biguanide benzoyl chitosan and biguanide benzoyl oligomeric chitosan was discussed.The structure of the low molecular weight biguanide benzoyl chitosan was analyzed by the infrared spectrum. The results showed that in  degradation temperature of 65 ℃, H2O2 mass percent concentration of 3.0% and  hydrochloric acid concentration of 1.0 %, the reaction time will lead to the molecular weights of the products, oligomeric chitosan or biguanide benzoyl chitosan, were relatively decreased ,and the substitution degree of the guanidino group were also reduced, but the basic structure of the main chain of degradation products did not be changed by infrared spectroscopy.