The invention relates to a preparation method of using microwave enzyme to prepare chitosan oligosaccharide product with the small molecular weight taking hexa-oligosaccharide as the main body in a compound way, which belongs to the biochemistry field of the chitosan oligosaccharide product preparation from chitosan. Chitosan material is dissolved with acetic acid, the weight percentage of the concentration of chitosan in the acetic acid solution occupies 2 percent to 7 percent, after chitosan A enzyme is added, the weight ratio of the chitosan A enzyme and the chitosan zymolyte occupies 0.05percent to 0.5 percent; the mixture is put in the microwave field, the power of the microwave field is 1000 W to 2000 W, compound degradation reaction is performed when the temperature is raised at 30 DEG C to 60 DEG C, and after the reaction is finished, firstly millipore filtration is conducted, afterwards the film of a molecular sieve is used for filtration, and after the working procedures of low temperature vacuum concentration and spray drying, the yellowish chitosan oligosaccharide product is obtained, the weight average molecular weight between 500 to 5000 can be controlled, the hexa-oligosaccharide proportion is high, the deacetylation degree is 80 percent to 90 percent, and the recovery ratio is 90 percent to 95 percent.