The present invention discloses a passive optical network system based on wavelength protection and the protection backup method thereof. It comprises an optical line terminal (OLT) with two interface circuits, two trunk lines, an optical splitter network, multiple branch lines and optical network units (ONU), each of which is with two interface circuits. The two interface circuits of the OLT transmit downlink optical signals with different wavelengths, while the two interface circuits of the ONU transmit uplink optical signals with different wavelengths. Each trunk line is set with a wavelength division multiplexing (WDM) device and it can only pass the uplink and downlink signals of the connected interface circuits. Each branch line includes a branch optical fiber and a WDM device that is used to transmit two downlink signals to the corresponding interface circuits respectively and meanwhile transmit uplink signals from the two interface circuits as well, so as to form two active/backup bidirectional optical paths between the corresponding interface circuits of the OLT and the ONU. The cost of setting up the system in the present invention is low, but the system can provide hot backup protection for the trunk optical fiber and the OLT.