This paper describes the implementation of the single carrier-frequency domain equalization by using the Field Programmable Gate Array(FPGA) devices of Xilinx Company. The implementation of the bursted structure of Fast Fourier Transform(FFT)/Inverse FFT(IFFT) and the lookup table of division are proposed. The synthesis tool embedded in the Integrated Software Environment(ISE) is adopted to synthesize the whole system,and check the resource consumption of the two methods. It is indicated that the proposed two methods can decrease the resource consumption by comparison to traditional methods. The feasibility of the entire program is verified by the simulation on the frequency domain equalization system.