The invention discloses a method for preparing indigo naturalis. The method comprises the following steps: selecting leaves or stem leaves of jacobinia suberecta baphicacanthus cusia, polygonaceae plant indigo or crucifer isatis tinctorial, extracting in hot water, and filtering to remove leave residues to obtain filtrate; adding an acid solution into the filtrate, and performing hydrolysis; adding an alkali solution to adjust the pH value of the solution to be 6-8 after hydrolysis is completed, standing, removing supernate to obtain precipitate, washing to be neutral, and drying to obtain theindigo naturalis. According to the preparation method, a new way for preparing indigo naturalis is provided, the influence of CaCO3 can be avoided, the labor intensity for preparing indigo naturaliscan be greatly reduced, and the production cycle can be shortened. By utilizing the preparation method, the content of indigo is 30.51-54.84 percent, the content of indirubin is 5.41-13.52 percent, the content of indigo is increased by 10-20 times that by a traditional processing method, and the content of indirubin is increased by 20-30 times that by the traditional processing method, and the quality of indigo naturalis products realizes qualitative leap.