In the TDOA target generation system， microwave photon links are used to transmit multi-channel and multi-band target simulation signals containing accurate TDOA information. To ensure the accuracy of TDOA information is enough， it is necessary to accurately measure the propagation delay of the target simulation signal through the photon link. A novel method for measuring the propagation delay of photon link is proposed in this paper， which uses a dedicated delay measurement chip based on the gate delay counting principle to achieve high-resolution and high-precision measurement. By occupying the same optical transmission channel of a single fiber through time sharing between the delay measurement signal and the target simulation signal， the measurement of the propagation delay and the transmission of the target simulation signal are achieved for a photon link， it meets the hardware requirements for accurately measuring the propagation delay of photon link mechanically. The experimental results show that this method can accurately measure the propagation delay of the TDOA target simulation signal through the photon link， with an error of less than 1ns， which is one order of magnitude higher than the TDOA measurement accuracy of the sensor， meets the measurement accuracy requirement of the system.