In view of the phenomenon that there is obvious noise in the results of the common view time comparison calculated by the standard dual-frequency ionospheric-free pseudorange combination of BeiDou-2 B1I&B2I, which affects its short-term stability, the research on selecting the optimal dual-frequency combination from the available frequency signals of BeiDou-2 and BeiDou-3 is carried out in order to improve the performance of BeiDou common view time comparison. Based on the standard common view files generated by CGGTTS (Common GNSS Generic Time Transfer Standard) software, the common view time comparison test of GPS, Galileo, BeiDou-2 B1I&B2I, B1I&B3I and BeiDou-3 B1I&B3I, B1C&B2a dual-frequency ionospheric-free pseudorange combination between the National Time Service Center, Chinese Academy of Sciences (NTSC) and Institute of Photonics and Electronics, Czech Academy of Sciences (TP) has been completed, and the common view results of each dual-frequency combination are denoised with Vondark filtering, and the precision of common view time comparison is evaluated by calculating the RMS (Root Mean Square) of the filter residual. The results show that the noise of the common view time comparison calculated by the pseudorange of BeiDou-3 B1C&B2a combination is relatively small, and the RMS of the filter residual is about 46%, 52%, and 37% higher than that of BeiDou-2 B1I&B2I, B1I&B3I, and BeiDou-3 B1I&B3I combinations, respectively, which is equivalent to GPS P1&P2 combination, and close to Galileo E1&E5a combination. The short-term stability (< 1 d) of BeiDou-3 B1C&B2a comparison link is better than that of BeiDou-2 B1I&B2I, B1I&B3I, and BeiDou-3 B1I&B3I, and is equivalent to the stability of GPS P1&P2 and Galileo E1&E5a. The medium and long-term stability (> 1 d) of six common view time comparison links tends to be consistent.