A method and apparatus for allocating a frequency resource to each micro User Equipment (UE) in a hierarchical cellular mobile communication system are disclosed. The method includes acquiring information about traffic of each macro UE or a macro BS in a frequency resource allocated to the macro UE or the macro BS, first Signal-to-Noise Ratio (SNR) information about an SNR of a signal from the macro UE or the macro BS, measured at each micro UE and second SNR information about an SNR of a signal from the micro UE, measured at each micro BS, calculating throughput of the micro UE using the traffic information, the first SNR information and the second SNR information, determining a frequency resource to be allocated to the micro UE using information about the calculated throughput and allocating the determined frequency resource to the micro UE.