A system and method for VLAN configuration of an E-PON converts physical ONU port information to logical OLT port information to construct profile information of the logical OLT system and VLAN membership information based on the logical OLT port, and provides a VLAN service to the users of an optical subscriber network. Accordingly, the present invention allocates the users in the ONU systems belonging to the same OLT port to different VLAN groups, provides enhanced VLAN services for the E-PON users, causes the OLT to perform functions of managing the profile of the ONU systems and transferring information among the users of the ONU systems, and causes the ONU systems to operate as terminals performing a multiplexing/demultiplexing function rather than as a conventional two-layer switch.