An LED controller is used with a video source and at least one LED unit, and includes a control signal generator and a driver. The control signal generator performs pulse width modulation based on a first clock signal, a second clock signal and a data signal, which is generated by the video source, to generate at least one control signal. The first and second clock signals are independent of a vertical synchronization signal that is generated by the video source. The driver generates, based on the at least one control signal, at least one drive signal that is related to light emission of the at least one LED unit.