The joint use of multi-frequency signals brings new prospects for precise positioning and has become a trend in Global Navigation Satellite System (GNSS) development. However, a new type of inter-frequency clock bias (IFCB), namely the difference between satellite clocks computed with different ionospheric-free carrier phase combinations, was noticed. Consequently, the B1/B3 precise point positioning (PPP) cannot directly use the current B1/B2 clock products. Datasets from 35 globally distributed stations are employed to investigate the IFCB. For new generation BeiDou Navigation Satellite System (BDS) satellites, namely BDS-3 satellites, the IFCB between B1/B2a and B1/B3 satellite clocks, between B1/B2b and B1/B3 satellite clocks, between B1C/B2a and B1C/B3 satellite clocks, and between B1C/B2b and B1C/B3 satellite clocks is analyzed, and no significant IFCB variations can be observed. The IFCB between B1/B2 and B1/B3 satellite clocks for BDS-2 satellites varies with time, and the IFCB variations are generally confined to peak amplitudes of about 5 cm. The IFCB of BDS-2 satellites exhibits periodic signal, and the accuracy of prediction for IFCB, namely the root mean square (RMS) statistic of the difference between predicted and estimated IFCB values, is 1.2 cm. A triple-frequency PPP model with consideration of IFCB is developed. Compared with B1/B2-based PPP, the positioning accuracy of triple-frequency PPP with BDS-2 satellites can be improved by 12%, 25% and 10% in east, north and vertical directions, respectively.