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For the advantages of high integration, low power consumption, flexible configuration programming and short development cycle, FPGA is more and more used in the embedded system design. A power quality monitoring system based on FPGA is presented. The system uses FPGA and Linux as the hardware and software platform, and the FTP protocol to get the sampled data. It is controlled by the network. The core of the system is the Fast Fourier Transform (FFT) that uses the non-recursive complex sequence FFT. Experimental results show that the test design based on the Spartan 3E500 platform is reliable and effective. Finally, the influence of Cache and multi-thread in the computation time is also analyzed.