A timing control circuit and an operating method thereof are provided. The timing control circuit includes a first clock generating circuit, a second clock generating circuit and a control timing generating circuit. The control timing generating circuit is coupled to the first clock generating circuit to receive a first clock signal. The control timing generating circuit is coupled to the second clock generating circuit to receive a second clock signal. The control timing generating circuit starts timing from a first reference time point according to the first clock signal for determining a second reference time point. The control timing generating circuit starts timing from the second reference time point according to the second clock signal for determining a time point of a trailing edge of a current line pulse of a scan reference signal, wherein the current line pulse corresponds to a current scan line of a display panel.