Numerical modeling approaches are favored for performing long-term analyses of continuous prestressed concrete rigid-frame (CPCR) bridges due to the complexity and high cost of experimental testing on such structures. In this study, a refined numerical modeling approach is first presented and validated by comparing the field monitor data of an existing long-span CPCR bridge in China. Then, long-term deflection analysis—considering box girder cracks, concrete creep, joint damage behavior and prestress—is conducted based on the proposed refined modeling approach. It is found that the time-dependent loss of longitudinal prestress has the most significant influence on the long-term structural stiffness, while joint damage between different segments has limited impact on overall structural performance, especially for large-span bridge cases. The local stress distribution is significantly influenced by typical damage, albeit with a different scope of impact. Therefore, targeted reinforcement has to be performed to achieve satisfactory repair results under different damage conditions.