A synchronous backlight device and an operation method thereof are provided. The synchronous backlight device includes a pulse width modulation (PWM) control circuit and a backlight driving circuit. The PWM control circuit receives the video sync information from a video processing circuit and generates a PWM control signal. Wherein, the video sync information defines a plurality of video frame periods, the PWM control circuit at least divides each of the video frame periods into a first period and a second period, the lengths of the first periods of the video frame periods are equal to one another. The frequency of the PWM control signal in the first periods is different from the frequency of the PWM control signal in the second periods. The backlight driving circuit drives the backlight source of a display panel in accordance with the PWM control signal.