The invention discloses a method for preparing tagatose by using whole-cell catalysis. The method comprises the following steps of transferring plasmid containing an alpha-glucan phosphorylase gene (or cellulosic polysaccharide phosphorylase and cellobiose phosphorylase genes, or a sucrose phosphorylase gene), a phosphoglucomutase gene, a glucose phosphate isomerase gene, a 6-phosphate tagatose epimerase gene, and a 6-phosphate tagatose phosphatase gene into engineered escherichia coli, so as to obtain converted bacterial strain; inducing the converted bacterial strain to produce enzyme, and permeabilizing; mixing the permeabilized bacterial strain, establishing a whole-cell enzyme catalysis reaction system with starch or starch derivative (or mixture of cellulase and cellulose or cellulose derivative, or sugarcane), and performing the whole-cell enzyme catalysis reaction, so as to obtain the tagatose. The method has the advantages that the tagatose is prepared by the whole-cell catalysis; the cost is low, the pollution is low, the yield rate is high, and the like; the method is suitable for preparing the tagatose in a scale way.