The invention provides a method and apparatus for reconfiguring wavelength of the ONU. To be specific, the OLT sends a Deactivate_ONU-ID message to the ONU, the Deactivate_ONU-ID message including a reconfiguration flag, a new receive wavelength assigned for the ONU and a new transmit wavelength assigned for the ONU. After receiving the Deactivate_ONU-ID message from the OLT, the ONU discards the TC layer parameters related to the current wavelength channel, and determines whether the reconfiguration flag included in the Deactivate_ONU-ID message indicates the receive wavelength and the transmit wavelength of the ONU are required to be reconfigured. If so, then the ONU replaces its original receive wavelength and original transmit wavelength with its new receive wavelength and the new transmit wavelength included in the Deactivate_ONU-ID message, and enters initial state; and if not, then the ONU enters initial state directly.