BeiDou-3 global navigation satellite system (BDS-3) has officially provided positioning, navigation, and timing (PNT) services on 31 July 2020. The difference between BDS-2 and BDS-3 in signal modulation mode, signal characteristics, and satellite clock datum leads to the possible existence of inter-system bias (ISB) between BDS-2 and BDS-3, which becomes the key to affect the time-frequency transfer of BDS. In this contribution, taking the observations of BRUX, CEBR, USUD, WTZZ, and YEL2 stations as an example, five analysis centres (ACs) precise products (for instance, CNT, COM, ESA, GBM, and WUM) are used to evaluate the BDS-2 BII/B3I combined BDS-3 B1I/B3I, B1I/B2a, B1C/B2a, and B1C/B2a time-frequency transfer performance with ignore ISB (ISB NO ), estimating ISB as constant (ISB CT ), estimating ISB as a random walk (ISB RW ) and estimating ISB as white noise (ISB WN ) four kinds of estimation strategies. The results show that the ISB CT estimation strategy has the better performance than ISB NO , ISB RW, and ISB WN estimation strategies in BDS-2/BDS-3 combined time-frequency transfer; compared with ignoring ISB strategy, the standard deviation and frequency instability of ISB CT estimation strategy is decreased by 9.16% and 12.83% on average, respectively. Meanwhile, an ISB CT estimation strategy is recommended when using CNT, COM, ESA, and WUM precision products for BDS-2/BDS-3 combined time-frequency transfer.