The present invention discloses a noise filtering fractional-n frequency synthesizer and an operating method thereof. The noise filtering fractional-n frequency synthesizer comprises a filter, a frequency calibration loop, a phase calibration loop and a digitally controlled delay line. The filter receives a first frequency division signal and generates a filtered signal. The frequency calibration loop is coupled to the filter and generates a first control signal. The phase calibration loop is coupled to the filter and the frequency calibration loop, and generates a second control signal. The digitally controlled delay line is coupled to the phase calibration loop and receives the second control signal. Thus, quantization noise of the fractional-n frequency synthesizer can be reduced, and phase noise of the fractional-n frequency synthesizer can be improved. In addition, the system remains locked after the filter outputs the signal.