The invention provides a control method of a double winding large power motor-driven system based on IEGT. The method comprises steps that auto-disturbance rejection control on a rotating speed loop is employed, and a reference value of a double winding T-axis current mean value is calculated; a reference value of a double winding M-axis current mean value is calculated by a magnetic linkage loop through a P adjuster; an M-axis current and a T-axis current of a double winding six-phase current under a synchronous rotating coordinate system are respectively carried out, a mean value and a difference value of the M-axis current and the T-axis current of two sets of windings are respectively carried out, amplitude of a reference voltage vector is calculated according to the mean value and the difference value of the M-axis current and the T-axis current of the two sets of windings, and a reference voltage vector is acquired through rotation of the coordinate system; a nine-level phase shift carrier wave modulation algorithm is employed to acquire a six-phase voltage of the double winding motor. The method is advantaged in that through double winding MT-axis current loop mean value and different value control, an imbalance current problem caused by winding parameter inconsistency is avoided, and a new means is provided for double winding motor control.