A tunable optical network unit (ONU) for a multi-wavelength passive optical network (MW PON) system and an operation method thereof are provided. The tunable ONU includes a cyclic tunable filter configured to have cyclic wavelength transmission properties that allow all wavelength channels of both a downstream signal and an upstream signal and to vary a wavelength to pass therethrough; a wavelength splitter configured to split an upstream signal wavelength band and a downstream signal wavelength band; a photodetector element configured to detect a downstream signal that is transmitted through the wavelength splitter, passing through the cyclic tunable filter which is aligned to a specific downstream signal wavelength channel; and a tunable transmitter configured to output to the wavelength transmitter an upstream signal of a wavelength channel that is determined based on an aligned downstream signal wavelength channel of the cyclic tunable filter.