The system of peak time delay tracking is designed, which bases on peak count rate scanning method for single photon detector. By scanning the time range near the previous peak position, a group of data can be compared to find the biggest value for determining the new peak position. It implements the peak of real-time tracking experiment during 125 km optical fiber in the environment of rapidly changing temperature. In order to solve the precision problem which is limited by the long step, the system introduces the polynomial fitting method to increase the accuracy. The accuracy of the light pulse transmission time obtained by peak time delay tracking system is superior to that obtained by avalanche photodiode directly measuring method, which is proved by the comparison experiment of single passing and double passing real-time measurements.