A visual drive control method with multi-phase encoding includes the following steps. A plurality of flickering sequences are generated by an encoding process according to a reference phase and a plurality of shifting phases divided in time division under at least one phase shift state, then a display unit is driven to display corresponding optical images. An optic nerve of an organism is evoked by the optical images, such that the organism generates a corresponding biological signal. Next, a computation process is performed to a digital biological signal converted from the biological signal to acquire an average captured reference phase and an average captured shifting phase of the digital biological signal. Then, the frequencies and the phase states of the digital biological signal and the flickering sequences are compared to output a corresponding control signal. A visual drive control apparatus with multi-phase encoding is disclosed herein.