The invention discloses a preparation process of isatis root medical solution, comprising the following steps: firstly, isatis root decoction tablets are processed by a water extraction method, and an isatis root water extract is obtained; secondly, the isatis root water extract passes through an inorganic ceramic membrane with the pore diameter of 100nm to 50nm under the pressure of 0.05 MPa to 0.1 MPa; and thirdly, the isatis root water extract then passes through an organic membrane with the intercepted molecular weight of 3000 to 1500 under the pressure of 0.05 MPa to 0.15 MPa to obtain the isatis root medical solution. The preparation process can run under low temperature, has short production period, little energy consumption, high separation efficiency and accuracy, little environmental pollution and up-and-up product quality. Through initial calculation, the invention can save about 3.42 tons of steam and 0.35 tons of alcohol by treating each ton of isatis root medicinal materials.