In order to improve the anti-interference performance and precision of Sparse Fourier Transform (SFT) time delay estimation algorithm under low SNR conditions, a new SFT time delay estimation algorithm is proposed based on Generalized Second Cross Correlation (GSCC).The new algorithm performs the SFT operation on the signal, and then adds the GSCC algorithm improved by least squares fitting.The algorithm rapidly processes the signal while suppressing the interfering noise at the same time.In this way, the performance of the time delay estimation algorithm is improved.Simulation tests and field data verification both indicate that the improved algorithm has satisfying anti-interference performance and estimation precision.