BeiDou global navigation satellite system (BDS) began to provide positioning, navigation, and timing (PNT) services to global users officially on 31 July, 2020. BDS constellations consist of regional (BDS-2) and global navigation satellites (BDS-3). Due to the difference of modulations and characteristics for the BDS-2 and BDS-3 default civil service signals (B1I/B3I) and the increase of new signals (B1C/B2a) for BDS-3, a systemically bias exists in the receiver-end when receiving and processing BDS-2 and BDS-3 signals, which leads to the inter-system bias (ISB) between BDS-2 and BDS-3 on the receiver side. To fully utilize BDS, the BDS-2 and BDS-3 combined precise time and frequency transfer are investigated considering the effect of the ISB. Four kinds of ISB stochastic models are presented, which are ignoring ISB (ISBNO), estimating ISB as random constant (ISBCV), random walk process (ISBRW), and white noise process (ISBWN). The results demonstrate that the datum of receiver clock offsets can be unified and the ISB deduced datum confusion can be avoided by estimating the ISB. The ISBCV and ISBRW models are superior to ISBWN. For the BDS-2 and BDS-3 combined precise time and frequency transfer using ISBNO, ISBCV, ISBRW, and ISBWN, the stability of clock differences of old signals can be enhanced by 20.18%, 23.89%, 23.96%, and 11.46% over BDS-2-only, respectively. For new signals, the enhancements are −50.77%, 20.22%, 17.53%, and −3.69%, respectively. Moreover, ISBCV and ISBRW models have the better frequency transfer stability. Consequently, we recommended the optimal ISBCV or suboptimal ISBRW model for BDS-2 and BDS-3 combined precise time and frequency transfer when processing the old as well as the new signals.