The invention relates to a modulation depth optimization control system for a six-switch converter and a method thereof. The system is technically characterized by comprising two current detection modules, two voltage detection modules, two reference waveform generation modules, a reference current generation module and an operation state detection module, wherein outputs of the two current detection modules and the two reference waveform generation modules are connected to the operation state detection module, and output signals of the operation state detection module are modulated to form driving pulse signals for operation of the six-switch converter. According to the method, the current running state of the six-switch converter is detected, and when the six-switch converter is locatedin a modulation depth optimizable interval, upper and lower paths of reference modulation signals are adjusted. By judging the directions of the upper and lower paths of current and adjusting the positions of the upper and lower paths of reference modulation signals of the corresponding phase, the crossing of the upper and lower paths of modulation signals of the same phase in the same carrier interval is realized, the operation efficiency of the six-switch converter is improved, and the cost of the six-switch converter is reduced.