The time-dependent behavior of a typical three-span prestressed concrete (PC) continuous box girder bridge was analyzed to investigate the effect of non-uniform shrinkage and creep due to thickness differences among webs and top and bottom flanges in box girders. Considering time-varying effects of compressive strength and elasticity modulus of concrete, finite element models which simulated cantilever-construction by solid and beam elements were developed, respectively. A comparative study on structural displacement, concrete stress and tendon stress caused by uniform and non-uniform creep and shrinkage after bridge completion was peformed. Meanwhile, long-term deflection and tendon stress were compared with relevant values which were calculated according to the standard. And the time when tensile stress and crack resulting from vehicle load and non-uniform creep and shrinkage in the bottom flange appeared was estimated. The results show that compared with uniform creep and shrinkage, non-uniform creep and shrinkage have smaller influence on the long-term deflection at midspan, and have greater effect on the concrete stress, which should be concerned in design of box girders.