The invention relates to a high-efficiency method for preparing chitosan by microbial fermentation, and belongs to the technical field of chitosan microbial fermentation. The method comprises the specific steps that 200 g of potatoes, 20 g of glucose, 3 g of dipotassium phosphate, 1.5 g of magnesium sulfate and 2-6 g of shrimp shells are prepared into a potato culture medium for autoclaved sterilization; aspergillus oryzae is fermented with the potato culture medium for 3-4 days at 28-38 DEG C; aspergillus oryzae thalli and shrimp shells with partial proteins and calcium carbonate removed after fermentation are obtained separately; the aspergillus oryzae is treated with a NaOH solution to obtain the chitosan; the shrimp shells are treated with citric acid at first and then decalcified anddeacetylated with a NaOH solution to obtain the chitosan. The method is mild in condition, high in yield, environmentally friendly and low in energy consumption and cost.