For the discussion of the source, preparation and quality problems of Indigo Naturalis, the historical tradition and reality were summarized by literature survey and producing area investigation. Besides some quality problems, potential safety hazards were found out in some samples from market tested. Because lime could not be dislodged enough from Indigo Naturalis in the process of purification, the samples of Indigo Naturalis contained too much lime and showed strong alkalinity. It was suggested that the quality standard of Indigo Naturalis should be revised and revised and some detection projects and methods should be added into the standard. In addition, we suggested that the production access of Indigo Naturalis should be further defined.