Window interpolation algorithm based on Fast Fourier transform (FFT) was adopted to analyze the har- monics. The current harmonic detection system has many bottlenecks, such as large amount of operation, long calculation time and poor real-time performance. Then, a scheme that takes ZYNQ which integrates Field-Pro- grammable Gate Array's (FPGA) high speed data processing capability and ARM efficient digital information management capability as the main control chip was proposed. The FPGA technology was used to realize the window interpolation FFT algorithm. The harmonic analysis system was also established in the Vivado platform. The frequency, amplitude and phase of 50 harmonics were calculated by the ZedBoard development board e- quipped with ZYNQ chip, and the results are compared with that of Matlab simulation. The research results show that harmonic analysis by using this system has high accuracy.