A Time Wavelength Division Multiplexing-Passive Optical Network (TWDM-PON) system and a communication link method thereof are provided. The communication link method is a method whereby an Optical Network Unit (ONU) which has established communication link to one Optical Line Terminal (OLT) establishes communication link to a different OLT. The ONU receives a wavelength change instruction to change a wavelength thereof to an operating wavelength assigned to the different OLT, and change the wavelength in response to the wavelength change instruction to synchronize to a downstream signal of the operating signal. In addition, the ONU receives an upstream discovery grant signal from the different OLT, and transmits an acknowledgement message to notify the receipt of the upstream discovery grant signal, so that the ONU establishes communication link to the different OLT.