To analyze the impacts of creep and shrinkage effects on the behaviors of long‐span prestressed concrete box girder bridges, a new nonlinear analysis model of creep and shrinkage effects that comprehensively considered three‐dimensional (3D) characteristics and girder damage evolution was presented. A corresponding numerical analysis method was implemented into the ABAQUS user‐supplied subroutine; this method was verified by comparing the analytical results to the classical experimental results. Finally, a continuous rigid frame bridge with a main span of 220 m was taken as an engineering example, and the analysis results and in situ measured data of long‐term deflection were compared. The results show that the 3D characteristic and the nonlinear property of creep have significant impacts on the prediction of long‐term deflection.