The invention discloses a preparation method of a compound indigowoad root granular electuary. The method specifically includes the following steps of preparation of indigowoad root leaching liquid, enzymolysis, micro-biological degradation, freeze drying and prilling. The preparation method improves a traditional extraction process, and in the enzymolysis procedure, polysaccharide, free amino acid, adenosine and other effective components in the indigowoad root leaching liquid are extracted; micro-biological fermentative degradation is conducted to obtain alkaloid and other effective components, then a freeze drying technique is adopted for drying and water removal, and the effective components of indigowoad roots cannot be damaged at the same time, so that the problem that by adopting awater extraction and alcohol precipitation method, the dosage of ethyl alcohol influences the whole preparation process and the preparation stability is solved; the preparation method is simple, hightemperature reactions are not required, the effective components in the indigowoad roots are extracted to the maximum degree, the practicability is high, and the preparation method is suitable for industrialized production.