Fast Fourier transform(FFT),usually suffering from the problem of frequency spectrum leakage and picket fence effect, would not be suitable as the calibration algorithm of merging unit metering characteristics calibration device, the ratio error and phase displacement of the calibration device utilizing common FFT algorithm cannot satisfy the requirement of 0.05 accuracy class specification. This paper, based on common FFT, proposes two improved FFT algorithm, i.e., single line interpolation FFT algorithm with Hanning window and two-line interpolation FFT algorithm with Blackman window, these two algorithms were compared with the common FFT algorithm on labview platform, the simulation results manifest that the two-line interpolation FFT algorithm with Blackman window has the highest accuracy for harmonic analysis, which is more suitable for merging unit metering performance calibration. Finally, A prototype calibration device using this algorithm is calibrated at National High Voltage Metering Station, the results show that the device can meet the specification of 0.2 accuracy class, confirming the effectiveness and feasibility of the two-line interpolation FFT algorithm with Blackman window.