Differential code biases (DCBs) are important parameters in GNSS (Global Navigation Satellite System) applications such as positioning as well as ionosphere remote sensing. In comparison to the conventional approach, which utilizes ground-based observations and parameterizes global ionosphere maps together with DCBs, a method is presented for GPS and BeiDou system (BDS) satellite DCB estimation using onboard observations from the Chinese Fengyun-3C (FY3C) satellite. One month worth of GPS and BDS data during March 2015 was exploited and the GPS C1C-C2W and BDS C2I-C7I DCBs were explored. To improve DCB estimation precision, the dual frequency carrier phase measurements leveled by code measurements were used to form basic observation equation. Code multipath errors of the FY3C onboard GPS/BDS observations were assessed and modeled as grid maps, and their impact on DCB estimation was analyzed. By correcting code multipath errors, the stability of DCB estimates was improved by 5.0%, 3.1%, 16.2% and 13.6% for GPS, and BDS geosynchronous orbit satellites (GEOs), inclined geosynchronous satellite orbit satellites (IGSOs) and medium Earth orbit satellites (MEOs), respectively. The monthly stability of FY3C-based DCBs was at the order of 0.1 ns for GPS satellites, 0.2 ns for BDS GEOs and 0.1 ns for BDS IGSOs and MEOs. By comparison to the ground-based DCB products issued by other institutions, FY3C-based DCBs showed stability degradation for BDS C02 and C05 satellites, while, for other satellites, the stability reached a similar or even superior level. The estimated FY3C receiver DCB stability was at the order of 0.2 ns for both GPS and BDS. In addition to the DCB estimates, the obtained vertical total electron content above the FY3C satellite orbit was also investigated and its realism was examined in physical and numerical aspects.