In order to solve the error of the weak grid impedance measurement based on the traditional Fourier transform, which is caused by the grid background harmonic interference and the fundamental frequency fluctuation, an improved detection method is proposed. By analyzing the mathematical characteristics of Fourier transform and window function, it is concluded that the slow frequency response attenuation speed of the traditional Fourier transform and signals’ asynchronous sampling is the main cause of the error. On this basis, a windowed Fourier transform algorithm is applied to greatly improve the Fourier transform attenuation speed from the main lobe to side lobe as well as from side lobe to side lobe. At the same time, the frequency resolution of Fourier transform is increased to avoid the main lobe interference caused by wide main lobe after windowing. Matlab simulation and experimental results verify that the method proposed is effective to improve calculation precision and anti-interference ability of grid impedance detection. This work is supported by Natural Science Foundation of Jiangsu Province (No. BK20130205).