In the complex environment,such as in mountainous area,under-ground,urban,in-door situations,the satellite navigation signal will be kept out,which makes the user’s receiver unable to receive enough navigation signal to position itself.Ground-Based Navigation System can flexibly deploy ground-based navigation based station according to different environment.It provides navigation signal with high quality to meet the user’s needs,so it increases the coverageof the navigation service.With the same principle as satellite navigation system,the user uses the ground-based navigation stations as time and space base to determine its position and time.Comparing with the satellite,the coordinate of ground-based navigation station can be obtained with higher accuracy,which makes the inter-station time synchronization become the very important factor to impact the precision of positioning.To achieve cost-effective and accurate inter-station time synchronization,a time and frequency lock method based on two-way time transfer is proposed in this paper,measurement error model is established,and the synchronization flow is established under the typical ground-based navigation signal framework,i.e.the ‘CDMA+TDMA’ framework.It not only realizes two-way time difference measurement and navigation signal transmission in the same time,but also tracks time-frequency change through time and frequency lock technology,as a result,the effect of troposphere delay can be reduced and the accuracy of time synchronization can be significantly improved.The simulation and experiment results show that the time synchronization accuracy is better than 1ns.