Abstract: To evaluate the long-term performance of the onboard rubidium clocks and passive hydrogen masers of the BeiDou-3 Navigation Satellite System (BDS-3), a systematic assessment of the frequency characteristics and stability of BDS-3 spaceborne atomic clocks was conducted based on precise clock offset products provided by multiple International GNSS Service (IGS) analysis centers. The influence of different clock products on clock performance evaluation results was also investigated. Precise clock products form the Center for Orbit Determination in Europe (CODE), Geo Forschungs Zentrum (GFZ) in Potsdam, Groupe de Recherche de Géodésie (GRG) Spatiale, the Information and Analysis Center (IAC), and Wuhan University Multi-GNSS Experiment Analysis Center (WUM) were selected for analysis. The evaluation was performed in terms of fitting residuals, frequency accuracy, frequency stability, and frequency drift rate. The results show that the root mean square errors (RMSE) of the fitting residuals from all five institutions reach the sub-nanosecond level and exhibit periodic characteristics, while the frequency accuracy achieves the order of 10⁻¹². In terms of frequency stability, the evaluation results obtained from different clock products show certain discrepancies. Among them, the IAC product exhibits the best daily stability, reaching 7.444 2×10⁻¹⁵, whereas the daily stabilities of the CODE, GRG, and WUM products are 1.631 0×10⁻¹⁴, 1.558 2×10⁻¹⁴ and 7.240 4×10⁻¹⁴, respectively. The GFZ product was slightly inferior at 1.111 1×10⁻¹³. Regarding the frequency drift rate, the average daily drift derived from all analysis centers reaches the order of 10⁻¹⁹, with the WUM product yielding the smallest drift. In addition, the average daily drift of passive hydrogen masers is significantly smaller than that of rubidium clocks. These results indicate that different IGS precise clock products can influence the absolute values of spaceborne atomic clock performance evaluation to some extent, whereas the overall variation trends and physical characteristics remain consistent.