A transformant is prepared to insert at least a gene expression cassette comprising a gene involved in the synthesis of 2-deoxy-scyllo-inosose into E. coli as host cells. A 2-deoxy-scyllo-inosose is synthesized from D-glucose, oligosaccharide, polysaccharide, starch and rice bran, using the transformant. A culture solution containing the 2-deoxy-scyllo-inosose is treated with a mixed bed or double bed type column comprising a hydrogen form of strong acidic cation exchange resin and an organic ion form of basic anion exchange resin. The 2-deoxy-scyllo-inosose as purified is reacted with trimethoxymethane to convert into 2-deoxy-scyllo-inosose dimethylketal, and the dimethylketal is crystallized and purified. Then, DOI is highly purified through hydrolyzing the dimethylketal in the presence of acid.