The accuracy of time synchronization can be significantly increased by enhancing the performance of atomic clocks. Future-generation time-frequency loads will be equipped with the latest ultrahigh-precision atomic clocks (with a day stability better than 10−17) and will leverage advantages of the space environment such as microgravity and low interference to operate a new generation of high-performance time-frequency payloads on low-orbit spacecraft. Moreover, using the high-precision time-frequency system of ground stations, low-time-delay high-performance time-frequency transmission networks, which have the potential to achieve ultrahigh-precision time synchronization, will be constructed. By considering full link error terms above the picosecond level, this paper proposes a new space-to-ground microwave two-way time synchronization method for scenarios involving low-orbit spacecraft and ground stations. Using the theoretical principles and practical application scenarios related to this method, a theoretical and simulation verification platform was developed to research the impact of the attitude, phase center calibration, and orbit determination errors on the single-frequency two-way time synchronization method. The effectiveness of this new method was verified. The results showed that when the attitude error is less than 72 arc seconds (0.02°), the phase center calibration error is less than 1 mm, and the precision orbit determination (POD) error is less than 10 cm (three-axis). After disregarding nonlink error terms such as equipment noise, this method can attain a space-to-ground time synchronization accuracy of better than 1.5 ps, and the time deviation (TDEV) of the transfer link is better than 0.7 ps @ 100 s, which results in ultrahigh-precision space-to-ground time synchronization.