The invention discloses a double-modulator control system of a medical electron linear accelerator. The double-modulator control system comprises a magnetron modulator, a grid-controlled electron gun modulator, a magnetron, a grid-controlled electron gun, an accelerating tube, three microwave detection circuits, a feedback microwave system, a therapeutic head, an automatic dosage control system and a digital signal processing system; the digital signal processing system is connected with the magnetron modulator and the grid-controlled electron gun modulator respectively, the magnetron modulator is connected with the magnetron, a microwave detection circuit is connected between the magnetron and the feedback microwave system, and the other two microwave detection circuits are connected between the inlet and the outlet of the accelerating tube and the feedback microwave system respectively; and the magnetron modulator, the three microwave detection circuits and the automatic dosage control system are connected with the digital signal processing system respectively, and the electron gun modulator is sequentially connected with the grid-controlled electron gun, the accelerating tube and the therapeutic head. The double-modulator control system realizes independent control, and can dynamically adjust the emission capacity of the electron gun in real time.