The present invention discloses an LED controller with de-flicker function and an LED de-flicker circuit and method thereof. The LED controller includes: a duty ratio calculation circuit for receiving a pulse width modulation (PWM) signal and generating a duty input signal, indicating a digital duty ratio of the PWM signal; an LED de-flicker circuit for receiving the duty input signal and generating a duty output signal wherein a noise in the duty input signal is filtered; and a dimming circuit for receiving the duty output signal and generating a dimming signal to control an LED circuit; wherein the duty output signal remains unchanged when the variation of the duty input signal is not larger than a hysteresis threshold, and the duty output signal follows the duty input signal when the variation of the duty input signal is larger than the hysteresis threshold.