The invention discloses prebiotic blueberry composite powder and a preparation method thereof. Blueberry powder with natural color, flavor and mouth feel is scientifically compounded with functional products including lactobacillus plantarum powder, honey powder, modified dietary fibers, enzyme powder, oligosaccharide and the like, so that the nutrition, the food safety and the health care functions of the blueberry composite powder are effectively improved, and besides, the prebiotic property and the quality stability of the blueberry composite powder are greatly improved. Compared with conventional blueberry composite powder, the prebiotic blueberry composite powder disclosed by the invention has the advantages that components are simple, the color, the flavor and the mouth feel are natural, the nutrient value is high, the health-care functions are powerful, the content of bioactive substances is high, the viable count of probiotics is high, the prebiotic property is strong, the kinds of functional metabolites of probiotics is complete, the content of the functional metabolites of the probiotics is high, the food safety is high, and the quality guarantee period is long.