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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 (ISB_NO), estimating ISB as random constant (ISB_CV), random walk process (ISB_RW), and white noise process (ISB_WN). 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 ISB_CV and ISB_RW models are superior to ISB_WN. For the BDS-2 and BDS-3 combined precise time and frequency transfer using ISB_NO, ISB_CV, ISB_RW, and ISB_WN, 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, ISB_CV and ISB_RW models have the better frequency transfer stability. Consequently, we recommended the optimal ISB_CV or suboptimal ISB_RW model for BDS-2 and BDS-3 combined precise time and frequency transfer when processing the old as well as the new signals.