The invention relates to a preparation method of instant isomaltooligosaccharide powder, and belongs to the technical field of preparation of food additive products. A technical scheme adopted in the invention is characterized in that the method comprises the following steps: carrying out size mixing on starch, liquefying, carrying out saccharifying glucoside conversion, carrying out decolorizing filtration, carrying out ion exchange, concentrating, and carrying out agglomeration spray drying to prepare type 50 instant isomaltooligosaccharide powder; or carrying out chromatographic separation before drying, carrying out ion exchange on an extract liquid, concentrating, and carrying out agglomeration spray drying to prepare type 90 instant isomaltooligosaccharide powder. The technical problems of easy moisture absorption agglomeration, uncontrollable density and unable instant solubilization of products produced through present isomaltooligosaccharide drying technologies are mainly solved in the invention. The isomaltooligosaccharide powder prepared in the invention has the advantages of uniform granularity, good fluidity, easy dissolution, unable moisture absorption, and expansion of the application of isomaltooligosaccharides in high-end fields.