The invention discloses a control method of an IQ modulator and a system thereof. The control method comprises the following steps of adding disturbance signals of a first disturbance frequency f1 and a second disturbance frequency f2 in an I bias voltage and a Q bias voltage of a light IQ modulator; detecting an output light signal output of the light IQ modulator and the added disturbance signals in real time, and monitoring direct current light power and calculating a correlation coefficient of the input disturbance signals and the output light signal; and using a light power value and the correlation coefficient to carry out feedback adjusting on the bias voltages of the light IQ modulator so that a bias state of the light IQ modulator satisfies an adjusting object. In the invention, through establishing connection between a bias voltage VI of an I path, a bias voltage VQ of Q path control and a bias voltage VP of a P path and the first disturbance frequency f1 and the second disturbance frequency f2, spectrum analysis in the prior art is replaced so that a calculating method is simplified; and an adjusting process possesses directivity, and a bias resolution of a control signal is less than 0.005Vpi.