In consideration of contributions from both carrier phase and pseudorange observations during computation, this study introduces a reconstructed method for estimating the multi-frequency global navigation satellite system (GNSS) inter-frequency clock biases (IFCB). Diverging from conventional approaches that separately calculate the time-varying and constant parts of IFCBs using carrier phase and pseudorange observations, the reconstructed method directly utilizes their combination to estimate satellite IFCBs. To validate the efficacy of the presented approach, 7 d observations from 87 International GNSS Service (IGS) stations are analyzed, with a specific focus on triple-frequency GPS, multi-frequency BDS-3, and Galileo IFCBs, aiming to scrutinize their distinctive characteristics. Furthermore, the performances of satellite IFCB estimation are investigated in both precise point positioning (PPP) and single-point positioning (SPP) using 35 IGS stations over 3 d. The results demonstrate that IFCBs of GPS BLOCK IIIA satellites exhibit centimeter-level variations, distinguishing them from BLOCK IIF counterparts. The Galileo IFCBs vary from millimeter to centimeter level, while those of BDS-3 reach a centimeter level. These variations significantly impact GPS PPP convergence performances but have minimal effects on Galileo and BDS-3 PPP. SPP performances are slightly enhanced when the time-varying IFCB part are taken into account. Additionally, we note disparities in the constant parts of satellite IFCBs computed with differential code bias (DCB) products, reconstructed, and pseudorange observation-based methods, particularly for BDS-3 C2I/C6I-C1P/C5P and C2I/C6I-C1P/C6I combinations. The differences of IFCB estimated with different strategies, SPP and PPP performances show that the reconstructed method is better than others, and the IFCB accuracy decreases when computed with satellite DCB products.