The invention relates to a preparation method of low-molecular chitosan, which comprises the following steps: ultrasonically treating crab shells with diluted hydrochloric acid, adding deionized water to dilute the diluted hydrochloric acid, adding benzoic acid for continuous ultrasonic treatment, deproteinizing with low-concentration sodium hydroxide, washing, and thermally treating deacetylated wet chitosan with high-concentration sodium hydroxide, dissolving the wet chitosan in a diluted hydrochloric acid aqueous solution, adding into a three-electrode system which takes a graphite plate as an anode, foam titanium as a cathode and a silver/silver chloride electrode as a reference electrode, keeping a certain distance of 3-5cm between the anode and the cathode, keeping a constant point potential of-1.2 to-1.5 V, and electrolyzing for 0.5-1 hour. According to the method, the repeated deacetylation process of sodium hydroxide in the deacetylation process is simplified, the usage amount of sodium hydroxide is reduced, the deacetylation degree of the low-molecular chitosan prepared by combining one-step sodium hydroxide deacetylation with electrolysis is as high as 94.8%, the molecular weight is low and reaches about 2500, the molecular weight distribution is narrow, the molecular weight distribution coefficient is 1.13, and the content of protein impurities in the low-molecular chitosan is as low as 0.072%.