One embodiment of the present invention provides a system that facilitates automatic adjustment of logical channels in a Fiber Channel (FC) network. During operation, the system receives FC data frames. A respective data frame is associated with a logical channel. The bandwidth on an FC link can be allocated into a plurality of logical channels, and a respective logical channel is associated with a dedicated buffer and can transport a plurality of data flows with data frames of variable length. The system then identifies a slow data flow in a first logical channel. Next, the system assigns the slow data flow to a second logical channel, thereby preventing the slow data flow from slowing down other data flows in the first logical channel. The system subsequently forwards the data frames in the slow data flow on the second logical channel onto an outgoing link.