An active duct noise control system and a method thereof are provided, including a duct, a noise source speaker, a microphone, a plurality of noise-cancelling speakers, and a plurality of controllers. Wherein, the noise source speaker generates the primary noise, and the microphone is disposed to receive the residual noise. The plurality of noise-cancelling speakers are disposed between the noise source speaker and the microphone and respectively generate noise-cancelling audio frequencies to offset the primary noise and reduce the residual noise. The plurality of controllers are respectively connected to the plurality of noise-cancelling speakers and the noise source speaker and calculate each of the noise-cancelling audio frequencies generated by each of the plurality of noise-cancelling speakers according to the multi-channel inverse filtering principle.