Precise point positioning (PPP) using the Global Navigation Satellite System (GNSS) phase and code measurements has become the primary technique for time and frequency comparisons. Several scholars have studied multi-GNSS PPP clock comparisons; however, the inconsistent pseudorange bias from receivers with different correlator spaces and front-end designs in pseudorange observations has not been considered. In this study, we analyze the characteristics of the inconsistent biases of the Global Positioning System (GPS) and BeiDou Navigation Satellite System (BDS) and their effects on PPP frequency transfer. The biases are confirmed to exist in receivers from Septentrio, Trimble, Leica and differ by manufacturer. To explicitly investigate the pseudorange bias effects of GPS and BDS on the PPP time and frequency comparisons, nine stations with receivers from three different manufacturers that could track the BDS-2 and BDS-3 signals were selected. Regarding PPP frequency transfer with inhomogeneous receivers, the Modified Allan Deviations (MDEVs) of the GPS and BDS PPP frequency stabilities were significantly optimized after using bias corrections. According to the receiver type classification strategy, the overall improvements in frequency transfer with Trimble-Septentrio and Trimble-Leica can be reached up to 31%, 29%, and 39%, and 38%, 29%, and 31% for GPS, BDS-2, and BDS-3, respectively. Moreover, the convergence time of the clock comparisons was shortened after bias corrections were applied. For GOPE-BRUX and GOPE-MATE links, the corrected cases yielded average clock difference stability improvements of 38%, 35%, and 53% and 35%, 35%, and 23% for GPS, BDS-2, and BDS-3, respectively. The results show that bias corrections are vital and allow for more stable time links for PPP frequency transfer.