In view of the fact of natural chitosan being insoluble in water, chitosan was rapidly oxidized and degraded by microwave assisted H2O2/UV system in experiment, with different low molecular weight water-soluble chitooligosaccharides prepared, while the molecular weight, molecular structure and water solubility of chitooligosaccharides were characterized. The experimental results showed that natural chitosan degraded rapidly within 5 min in the microwave-assisted H2O2/UV system. The prepared chitooligosaccharides had good water solubility in a wide range of pH. FTIR results indicated that the chemical structures and functional groups of the water-soluble chitooligosaccharides were consistent with the chitosan raw materials; XRD results showed that H2O2 played a significant role in destroying the crystalline structure of chitosan and improved the water solubility of chitooligosaccharides. TG results showed that the thermal stability of the water-soluble chitosan crystallization zone was deteriorated after it had been destroyed.