A time synchronization system based on the dual fiber unidirectional wavelength division multiplexing technology is proposed. The master and slave stations of the system are connected by dual optical fiber links. Four time interval counters are used to measure the transmission delay of two wavelengths and four time signals,and the clock difference of master-slave station can be accurately measured. This method can eliminate the influence of ambient temperature on fiber length,refractive index and transmission group delay. The master and slave stations are connected by100km and 90km optical fibers respectively. When the temperature of optical fiber link changes from - 20℃ to 40℃,the clock difference estimation error of master and slave stations can be reduced by about 1.3 ns with 1310～1550 nm wavelength,and the time service accuracy can be improved by about 200 ps with 1490～1550 nm wavelength.