A backlight module driving system and a driving method thereof are applied to a Liquid Crystal Display (LCD). In the LCD, a timing controller obtains a three-dimensional (3D) image signal provided by a graphics processor, generates a Liquid Crystal (LC) driving control signal, and generates a corresponding light adjusting signal according to a data writing time and a Vertical Blanking Interval (VBI) time of the LC driving control signal. A backlight driver obtains and analyzes the light adjusting signal, so as to disable a backlight module during the data writing time, and enable the backlight module during the VBI time.