A method, system and apparatus for managing alarms in a Long Reach Passive Optical Network (LR-PON) system are disclosed. The method includes: obtaining a PON signal from an Optical Line Terminal (OLT) or an Optical Network Unit (ONU) on one side; checking whether the obtained PON signal fails; and notifying the ONU or the OLT on the other side if the PON signal fails. The method, system and apparatus under the present invention monitor the LR-PON transmission quality and process various alarm indications raised in the LR-PON signal monitoring.