The currently available triple-frequency signals give rise to new prospects for precise point positioning (PPP). However, they also bring new bias, such as time-varying parts of the phase bias in the hardware of receivers and satellites due to the fact that dual-frequency precise clock products cannot be directly applied to triple-frequency observation. These parameters generate phase-based inter-frequency clock bias (PIFCB), which impacts the PPP. However, the PIFCBs of satellites are not present in all GNSSs. In this paper, various IF1213 PPP models are constructed for these parts, namely, the triple-frequency PIFCB (TF-C) model with PIFCB estimation, the TF inter-frequency bias (IFB) (TF-F) model ignoring the PIFCB, and the TF-PIFCB-IFB (TF-CF) model with one system PIFCB estimation. Additionally, this study compares these IF1213 PPP models with the dual-frequency ionosphere-free (DF) model. We conducted single system static PPP, dual-system static and kinematic PPP experiments based on BDS/GPS observation data. The GPS static PPP experiment demonstrates the reliability of the TF-C model, as well as the non-negligibility of the GPS PIFCB. The BDS static PPP experiment demonstrates the reliability of the TF-F and TF-CF models, and that the influence of the BDS-2 PIFCB can be neglected in BDS. The BDS/GPS PPP experimental results show that the third frequency does not significantly improve the positioning accuracy but shortens the convergence time. The positioning accuracy of TF-C and TF-CF for static PPP is better than 1.0 cm, while that for kinematic PPP is better than 2.0 cm and 4.0 cm in the horizontal and vertical components, respectively. Compared with the DF model, the convergence time of the TF-C and TF-CF models for static PPP is improved by approximately 23.5%/18.1%, 13.6%/9.7%, and 19.8%/12.1%, while that for kinematic PPP is improved by approximately 46.2%/49.6%, 33.5%/32.4%, and 35.1%/36.1% in the E, N and U directions, respectively. For dual-system PPP based on BDS/GPS observations, the TF-C model is recommended.