In order to fully consider the influence of differential shrinkage on the long-term deflection of a long-span continuous rigid-frame concrete bridge, formulas for calculating equivalent shrinkage strain were deduced based on a normal section assumption. Bar-system FEM (finite element method) was used to calculate the long-term deformation of Sutong continuous rigid-frame bridge due to differential shrinkage, and the equivalent shrinkage strain was simulated with the cooling method. The research results show that when the effect of differential shrinkage is considered the deflection at mid-span of Sutong continuous rigid-frame bridge is 6.0 cm larger than that based on the conventional method. The long-term deflection due to differential shrinkage resulted from different thicknesses of flanges is up to 5.5 cm, while it is only 0.5 cm due to differential shrinkage resulted from different ratio of reinforcement. The deformation due to differential shrinkage is significant and should be considered in camber setting of long-span concrete box girder bridges.