The accuracy of ultra-rapid orbits is a key parameter for the performance of GNSS (Global Navigation Satellite System) real-time or near real-time precise positioning applications. The quality of the current BeiDou demonstration system (BDS) ultra-rapid orbits is lower than that of GPS, especially for the new generational BDS-3 satellites due to the fact that the availability of the number of ground tracking stations is limited, the geographic distribution of these stations is poor, and the data processing strategies adopted are not optimal. In this study, improved data processing strategies for the generation of ultra-rapid orbits of BDS-2/BDS-3 satellites are investigated. This includes both observed and predicted parts of the orbit. First, the predicted clock offsets are taken as constraints in the estimation process to reduce the number of the unknown parameters and improve the accuracy of the parameter estimates of the orbit. To obtain more accurate predicted clock offsets for the BDS’ orbit determination, a denoising method (also called the Tikhonov regularization algorithm), inter-satellite correlation, and the partial least squares method are all incorporated into the clock offsets prediction model. Then, the Akaike information criterion (AIC) is used to determine the arc length in the estimation models by taking the optimal arc length in the estimation of the initial orbit states into consideration. Finally, a number of experiments were conducted to evaluate the performance of the ultra-rapid orbits resulting from the proposed methods. Results showed that: (1) Compared with traditional models, the accuracy improvement of the predicted clock offsets from the proposed methods were 40.5% and 26.1% for BDS-2 and BDS-3, respectively; (2) the observed part of the orbits can be improved 9.2% and 5.0% for BDS-2 and BDS-3, respectively, by using the predicted clock offsets as constraints; (3) the accuracy of the predicted part of the orbits showed a high correlation with the AIC value, and the accuracy of the predicted orbits could be improved up to 82.2%. These results suggest that the approaches proposed in this study can significantly enhance the accuracy of the ultra-rapid orbits of BDS-2/BDS-3 satellites.