Measurement time-tag error affects the precision of Dual-one-way ranging (DOWR) directly. For DOWR applied in deep-space, which have no access to GPS, autonomous time synchronization method is more valuable. In this paper, a method based on two-way time transfer (TWTT) for time synchronization is introduced, and the requirement of TWTT for DOWR is studied. The theoretic precision of PRN-code-based and carrier-phase-based TWTT is analyzed, which shows the combination of the carrier phase and PRN code phase can provide competent time synchronization for DOWR. The system design of a DOWR prototype system integrated with S-band TWTT system is presented. The experiments based on the system indicate that the proposed method is a potential method of autonomous time synchronization for deep space DOWR applications.