In response to the increasingly wide-ranging requirements for high-precision time synchronization systems, a high-precision time synchronization method for BeiDou-3 navigation satellite system (BDS-3) receivers is proposed. This time synchronization method runs on a BDS-3 navigation chip developed by our company. A closed loop time synchronization method similar to the digital carrier loop is used, in which PVT is equivalent to a phase discriminator and a frequency discriminator、a pulse per second(PPS) output control module is equivalent to a numerically controlled oscillator（NCO） and third-order phase-locked loop assisted by second-order frequency-locked loop is applied. By the experience in this paper, the time synchronization accuracies of one hour and one day are 2.64ns and 3.83ns. The experimental results show that the time synchronization accuracy of the method is improved without increasing hardware resources.