An intra-system bias (ISB) is a necessary parameter in the BeiDou Navigation Satellite System (BDS)-2 and BDS-3 integrated precise point positioning (PPP); however, its influence in BDS-2/BDS-3 combined processing remains unclear. This paper investigates the ISB effects on the combined PPP using different precise orbit and clock products. Considering an increasing number of BDS products, a comprehensive evaluation of the products is undertaken before validating with PPP tests. Results indicate that BDS-2 Wuhan University (WUM) orbital differences outweigh Centre National d’Etudes Spatiales (CNT), Shanghai Observatory (SHA), and Information and Analysis Center (IAC) orbits. Moreover, BDS-3 constellation registers better clock performance than BDS-2 using any MGEX product. Furthermore, introducing the ISB into the combined processing of BDS-2 and BDS-3 improves both the positioning performance and convergence time for all products. The best improvement in positioning performance is achieved when Deutsches GeoForschungsZentrum (GBM) product is employed. Finally, it is found that considering the ISB in the PPP model affects the code more than the phase observations.