A method and apparatus for mapping a resource unit in a wireless communication system is provided. The method includes obtaining a frequency partition (FP) count (FPCT), an size of FPi (FPS) for i>0, and subband (SB) count of FPi (FPSC) for i>0 (where FPi is an ith FP), obtaining a value KSB,FPi indicating an SB count for FPi and a value KMB,FPi indicating a miniband (MB) count for FPi on the basis of the FPCT, the FPS, and the FPSC, and mapping an SB PRU including a plurality of contiguous physical resource units (PRUs) and an MB PRU including a plurality of contiguous PRUs to each FP in a granularity of a PRU set on the basis of the values KSB,FPi and KMB,FPi. Each FP can obtain a frequency selective scheduling gain based on the SB and a frequency diversity gain based on the MB.