A digital signal processing device of a base station configured to process down-link signals in a wireless communication system employing orthogonal frequency division multiple access (OFDMA) and a method of processing data in the device are provided. The device includes a clock controller configured to monitor whether a signal is allocated to an input and control a frequency of clocks to have a first or second characteristic based on the monitored result, and a data processor configured to process the input, and synchronize with the clock controlled by the clock controller.