Supercritical carbon dioxide modified with acetonitrile and water for the extraction of indirubin and tryptanthrin from Folium Isatidis and the collection of these two bioactive ingredients by a spray mode are presented in this study. Two pumps, one for the addition of the modifier and the other for the transportation of CO2, were used for supercritical fluid extraction (SFE). This is a fast and environmentally-friendly approach for the production of herbal medicine. Compared to conventional solvent extraction, the yield of bioactive indirubin and tryptanthrin by this SFE process was approximately the same, but with a shorter process time and better protection of the environment.