Abstract: The decaying DC component affects the accuracy of full cycle discrete Fourier transform(FCDFT) when detecting fault currents in power system. In order to solve this problem, an improved algorithm is proposed for saturation test under high current for current transformer detection system based on LabVIEW. Firstly, through the simulation by the saturation test under high current for current transformer detection system, the parameters of the decaying DC offset is identified. And then the original current could be obtained with FCDFT algorithm, then using the sampling values minus the decaying DC component to get the corrected sample values. It is proved that the proposed method has higher accuracy for the fundamental component, and it is suitable for acquisition and measurement software based on LabVIEW.