A gain controlling system, a sound playback system, and a gain controlling method thereof are disclosed. The gain controlling system includes a main gain control unit, a sub gain control unit, and a logic control unit. The main gain control unit has a first step-by-step adjusting magnitude; the sub gain control unit has a second step-by-step adjusting magnitude; wherein the second step-by-step adjusting magnitude is smaller than the first step-by-step adjusting magnitude. The logic control unit is used for controlling the main and the sub gain control unit to transform an analog signal into a converted signal according to an adjustment command signal and further determining whether an adjusting magnitude required by the adjustment command signal is larger than a maximum gain range of the sub gain control unit. If yes, the logic control unit controls the main control unit and the sub gain control unit repeatedly.