The invention relates to a method for preparing chitosan into water-soluble chitosan oligosaccharide, which takes the chitosan as raw material and comprises the following steps of: treating the chitosan by rinsing and drying technique, and then soaking in material liquid prepared by purified water and food grade hydrogen peroxide; carrying out microwave radiation degradation treatment, and formingthe mixed liquid of low molecular weight chitosan oligosaccharide which can be dissolved in the material liquid and chitosan part of which is not dissolved; after that, filtering and obtaining the residue of the chitosan and the chitosan oligosaccharide solution; and finally, adding the chitosan oligosaccharide solution into absolute alcohol for alcohol precipitation, and then carrying out suction filtration and drying, thus obtaining the finished product of the water-soluble chitosan oligosaccharide. By adopting the microwave radiation degradation treatment technology and exciting energy bya physical method, the higher molecular weight chitosan is degraded into the low molecular weight water-soluble chitosan oligosaccharide with stable structure, no reaction by-product is generated in the degradation process, and no contaminant is produced; furthermore, compared with the preparation method in the prior art, the method has the advantages of advanced technique, simple working procedures, little production facility investment, high purity of the product, stable quality and the like, thus opening up wide market application prospect for preparing the chitosan oligosaccharide by taking the chitosan as raw material.