BeiDou navigation satellite system (BDS-3) has begun to provide stable high precision positioning, navigation and timing service for global users. In this paper, based on China′s time reference system of UTC (NTSC), the performance analysis of BDS-3 undifferenced combined carrier phase time comparison is carried out. The performance of BDS-3 undifferenced combined carrier phase time comparison in zero and long baseline, and the BDS-3 and GPS fusion carrier phase time comparison are carried out and studied by using data of BDS-3. Results show that the standard deviation of zero baseline and common clock comparison between two receivers is smaller than 0. 3 ns. For the long baseline time, the time difference between the Asia-Europe two time keeping laboratories by using BDS-3 undifferenced combined carrier phase time comparison, and the fusion carrier phase time comparison have a good consistency with the results released by International Bureau of Weights and Measures (BIPM) with GPS link. The frequency stability and time stability of result are basically the same as BIPM, and the root mean square of the residual is smaller than 0. 25 ns. Experimental results meet the application requirements for sub-nanosecond time comparison.