Precise phase difference measurement is critical for distributed time synchronization systems. Aiming at the problem of how to realize the sub-nanosecond phase difference measurement of the time signal, the digital dual mixer time difference (DDMTD) measurement technology is used to measure the fine transmission delay and the two digital clock phase difference. Given the problem that it is difficult to generate a common clock source with fine frequency changes inside the FPGA chip, the Si5338 chip is used to generate 4 differential clocks, and the communication with the FPGA is completed through the I2C protocol, and the differential signal is converted into a single-ended clock source inside the FPGA as two The common standard frequency of clock signals with the same frequency and different phases, realize the amplification of the phase difference measurement range, making the measurement accuracy reach sub-nanosecond level.