The transmission line affected by the flow transfer will enter a state of overload operation. The setting value of the distance backup protection needs to avoid the minimum load impedance. As a result, the flow transferring will bring significantly impacts to the distance backup protection. Focusing on this situation, this paper raises a distance backup protection setting scheme to cope with the flow transferring. This scheme is based on the wide area protection system. First, the WAMS is used to quickly calculate the apparent impedance value on the transmission line. Then, the flow transfer ratio on the lines is calculated according to the variation of the apparent impedance. For lines of different states of overload, the corresponding setting values adjustment method is used for backup protection. The adjustment method can not only prevent the mistake actions of the backup protection on the overload lines, but also can identify the short-circuit faults on the lines which are protected. At last, the setting information and load fluctuation are uploaded to the dispatch center as auxiliary information. So that the dispatch center can make a decision about the load control. On the basis of this decision, the setting value of the backup protection is further adjusted until the transmission line is returned to the normal state of load. The New England 10-unit 39-bus system is taken as an example. This method is verified by the BPA simulation.