The invention discloses a method for preparing isomalto-oligosaccharide from glucose BD liquor. The method comprises the following steps: (1) glucose BD liquor preparation,(2) decolorization and filtration, (3) ion exchange, (4) glucoside conversion, (5) enzyme deactivation, (6) filtration, (7) decolorization, (8) ion exchange and (9) steaming: a discharged material after ion exchange in the step (8) is pumped into a five-effect falling-film evaporator for evaporation and concentration until the mass percent concentration of the material is 70-75% to prepare isomalto-oligosaccharide, wherein the discharge temperature ranges from 80 DEG C to 85 DEG C. Compared with the prior art, the method has the benefits that waste liquor (BD liquor) after chromatographic separation of glucose mother liquor in a crystal glucose production process is taken as a raw material, so that local materials are used, wastes are turned into wealth, and the glucose mother liquor in the crystal glucose production process is comprehensively utilized by 100%; the effects of no pollution and zero emission are achieved; the added value of a product is increased.