In the background of strong impulse noise, the performance of fractional low-order statistics delay estimation method is degraded and the prior knowledge of noise is required. In order to solve the problem, a new time delay estimation method based on second-order fractional loworder covariance is proposed. Firstly, the bounded nonlinear sigmoid function is used to process the signal with impulse noise, so that the additional impulse noise can be fully compressed without affecting the time delay information carried by useful signals. Then, the second-order fractional low-order covariance operation is carried out on the processed signals of receival and transmission, that is, after obtaining the self-fractional low-order covariance of the transmitted signals and the mutual fractional low-order covariance of the received and transmitted signals, the mutual fractional low-order covariance of the two is calculated again, thus, the effect of impulse noise can be further suppressed. Finally, the effectiveness of the proposed method is verified by simulation experiments. The results show that the proposed method is free from the restriction that the fractional low-order covariance index is less than the characteristic index of Alpha stable distribution noise, and has higher estimation accuracy than the fractional low-order covariance method. The simulation experiment results show that under the generalized signal-to-noise ratio of -10 dB, the delay estimation takes 0.056 0 s and the accuracy reaches 97.76%.