The invention belongs to the chemical engineering industry and discloses a method for preparing carboxymethyl chitosan by micro-aqueous phase. The method is as follows: taking chitosan as raw material, firstly alkalifying the chitosan, then carrying out carboxylation reaction, adjusting the pH value, washing, drying and crushing, thus obtaining the carboxymethyl chitosan product. When the method is used for preparing the carboxymethyl chitosan, no organic dissolvent is added; after the carboxylation reaction, the product with higher substituted ratio can also be obtained without needing water for dilution, centrifugalization and organic solvents such as alcohol and the like for settling out; in the method, the carboxylation reaction is completely carried out, precipitates insoluble in water are few and the system is in the mini-amount water semi-wet state, thus greatly reducing the cost. The method has the characteristics of simple and convenient operation, few equipment investment, low cost, energy saving and emission reduction, suitable for industrialization production and the like.