Satellite and ground station time synchronization is the key technology of navigation satellite system. Two-way time comparison method between satellite and ground station clocks can improve the accuracy of satellite and ground station time synchronization effectively. By analyzing the influence of satellite-to-ground station range variation on two-way time comparison, which is the source of hundred nanoseconds error, a method of observe data differential correction was presented. Numerical simulation performed later shows that this method can reach the level of nanosecond precision.