The invention provides a preparation method of composite protein powder with a high amino acid grade. The preparation method specifically comprises the following steps: performing micronization treatment on raw material protein by a colloid mill and/or a high-pressure homogenizer, heating the raw material protein to denature the protein, performing countercurrent ultrasonic assisted enzymatic hydrolysis through single protease or multi-enzyme combination, performing individual or joint fermentation of yeast, lactic acid bacteria and bacillus subtilis to remove stinking and peculiar smell, performing ultrafiltration and ion exchange resin desalting, evaluating and supplementing essential amino acids, performing enzymatic polymerization and reconstitution reaction, and performing drying or performing drying and mixing to obtain a high-quality protein product with a reasonable proportion of the essential amino acids and an amino acid grade being 95 or above. The obtained composite proteinpowder has the high essential amino acid grade, belongs to high-quality protein, is easy to digest and absorb, has low sodium content, is suitable for people who need the high-quality protein, elderly people with a low protein digestion function, and persons under rehabilitation; the protein powder with low contents of sodium, potassium and phosphorus is suitable for people suffering from chronickidney disease (CKD) and the like; the product also has the effects of resisting oxidation, lowering blood cholesterol, strengthening the body and enhancing immunity.