One embodiment of the present invention provides a method for facilitating asymmetric line rates in an Ethernet passive optical network (EPON) which includes a central node and at least one remote node. During operation, the system provides a downstream code-group clock, wherein each cycle thereof corresponds to a code group transmitted from the central node to a remote node. The system also provides an upstream code-group clock, wherein each cycle thereof corresponds to a code group received at the central node from a remote node. In addition, the system provides a multi-point control protocol (MPCP) clock, wherein the frequency ratio of the MPCP clock to the downstream code-group clock is different from the frequency ratio of the MPCP clock to the upstream code-group clock, thereby allowing the downstream transmission to be performed at a faster line rate than the upstream transmission line rate.