The present disclosure relates to a 5G or pre-5G communication system for providing a higher data rate after a 4G communication system such as LTE. Particularly, the present disclosure relates to pre-processing for Filter Bank Multi-Carrier (FBMC) in a wireless communication system, and a method of a communication node includes the operations of receiving a signal from a counterpart node, determining a pre-processing scheme according to a channel and a frequency confinement characteristic of a filter based on the received signal, and performing pre-processing for a subcarrier set corresponding to the filter in accordance with the determined pre-processing scheme.