Abstract: In present time delay estimation methods of FH signal, the problems like the models are narrowband model and the precision is confined by the sampling interval are widely exist. For this, a new method which used the phase difference in reference frequencies based on the characteristic of FH signal is proposed in this paper. It estimates FH signal’s time delay by the relation between phase difference and time delay. According to the result of experiments, this method isn’t confined by the sampling distance directly and the precision can reach peel seconds. Especially, it can also be used in other signals which have abundant information in frequency and easy implemented in engineering.