The invention provides a method for producing dihydroxyacetone through microbial transformation, which comprises the following steps: inoculating Gluconobacter oxydans CCTCC No:M 208069 into a fermentation medium for culture to obtain fermentation broth; taking cells containing enzyme in the fermentation broth as a catalyst and performing biocatalysis in a reaction system taking glycerol as a substrate; and after the reaction, separating and purifying reaction solution to prepare the dihydroxyacetone. The method utilizes integral cells as a biocatalyst, generates the DHA in an air stirred bioreactor by combining the integral cell coenzyme regeneration technology, has the characteristics of simple and convenient operation, energy conservation, high production efficiency and the like, and can be suitable for industrial mass production.