The performance of time-critical systems depends heavily on time synchronization accuracy. Therefore, it is crucial to have a synchronization method that can achieve high time synchronization accuracy. In this paper, we propose a new underlying transmission architecture and new synchronization messages. On the basis of these, aiming at the time error problem of the slave clock, we propose an enhanced time synchronization method based on new synchronization messages. Furthermore, we evaluate the performance of the enhanced time synchronization method on the OMNeT++ simulator. In addition, we compare the impact of different crystal oscillator accuracies and different crystal oscillator frequencies on time synchronization accuracy, respectively. Simulation results show that the time offset is at most ±1 clock period using the enhanced time synchronization method. We realize the purpose of timing the master clock and the slave clock by counting the period of the clock signal. Therefore, we needed to round down the time count to an integer. This is the reason why −1 and 1 appear at the same time. When the crystal oscillator frequency used is 80 MHz, the system can achieve a time synchronization accuracy of ±12.5 ns; that is, a nanosecond-level time synchronization accuracy can be achieved. With the reduction of the crystal oscillator accuracy of the slave clock, the synchronization accuracy of ±1 clock period can still be achieved. With the increase in the crystal oscillator frequency, the time synchronization accuracy that can be achieved also improves. The method proposed in this paper provides a new way of thinking and has certain guiding significance for improving the time synchronization accuracy of time-critical systems.