The invention discloses a technology for treating isatis tinctoria. The technology includes the following steps that A, roots and leaves of the isatis tinctoria are separated from the isatis tinctoria; B, a top cover is opened, and isatis roots and folium isatidis obtained from the isatis tinctoria are poured into a shell; C, a motor is started; D, an air blower is started; E, after air blowing isconducted for some time, the air blower is shut down, an exhaust fan is started, and the folium isatidis leaves from the shell through an exhaust pipe under negative pressure generated by the exhaustfan; F, after air exhausting is conducted for some time, the exhaust fan is shut down, the motor is shut down, and the isatis roots accumulate on the bottom face of the shell under the effect of gravity; G, a bottom cover is started, and isatis roots are taken out; H, a sieving plate is opened, aggregate is taken out, and the interior of the shell is cleared. Through the technology, the aggregate, the isatis roots and the folium isatidis are well separated, it is avoided that multiple machines are arranged, and as a result power consumption and work burdens are increased, and production efficiency can be effectively improved.