The global system of BDS (BeiDou Navigation Satellite System), i.e., BDS-3, is characterized with a multi-frequency signal broadcasting capability, which was demonstrated as beneficial for GNSS (Global Navigation Satellite System) data processing. However, research on real-time BDS-3 clock estimation with multi-frequency signals is quite limited, especially for the new B1C and B2a signals. In this study, we developed models for BDS-3 multi-frequency real-time data processing, including the uncombined model for clock estimation and the GFIF (Geometry-Free Ionosphere-Free) combined model for IFCB (Inter-Frequency Clock Bias) determination. Based on the models, simulated real-time numerical experiments with about 80 global IGS (International GNSS Service) network stations are conducted for validation and analysis. The results indicate that: (1) the uncombined model with multi-frequency signals can achieve comparable accuracy with the traditional dual-frequency IF model in terms of clock estimation, and the double-differenced clock STDs (Standard Deviations) are generally less than 0.05 ns with post-processed clocks as a reference; (2) unlike the B1C and B1I/B3I signals, the satellite IFCBs generated from multi-frequency clock estimation show apparent temporal variations for B2a and B1I/B3I signals, further investigation with GFIF models confirm the variations mainly result from the errors of receiver antenna corrections. Therefore, we addressed the feasibility of the uncombined model and the importance of accurate antenna information in the multi-frequency data processing.