The invention discloses environmentally-friendly wheat malt composite powder and a preparation method thereof. Wheat malt powder with natural color, flavor and mouth feel is scientifically compounded with functional products including lactobacillus plantarum powder, modified dietary fibers, enzyme powder, oligosaccharide and the like, so that the nutrition, the food safety and the health care functions of the wheat malt composite powder are effectively improved, and besides, the prebiotic property and the quality stability of the wheat malt composite powder are notably improved. The environmentally-friendly wheat malt 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 high, 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. In the wheat malt preparation process, ultrasonic cleaning, microwave instantaneous puffing for killing embryo, high voltage pulse, biologic enzymolysis united soaking and sprouting are adopted, so that soaking and sprouting time is short, the sprouting rate is high, the content of bioactive substances is high, the production efficiency is high, environmental pollution cannot be caused, and the environmentally-friendly wheat malt composite powder and the preparation method thereof are environmentally-friendly.