Based on the flanges’ different maximum shear angle differences selected as the shear-lag generalized displacements, the energy variational principle was applied to deduce the shear-lag differential equations for twin-cell box girders with and without shear deformation in consideration, and the initial parametric solutions of the box girder’s longitudinal stress and vertical deflection were given according to the boundary conditions. From the angle of mechanics and mathematics it was proved that the shear deformation and the shear lag were 2 relatively independent mechanical behaviors, of which the impacts on the box girder mechanics were expounded: the shear deformation had no effect on the longitudinal stress but had great influence on the vertical deflection. The example of a simply-supported box girder shows that the longitudinal stress at the middle cross section calculated with the presented analytic method and with the numerical method are in good agreement, of which the lateral distribution is similar to that in the case of single-cell box girders; however, the shear-lag effect around the side webs is slightly greater than that around the middle web. The shear deformation adds to the middle deflection of the box girder under concentrated and uniformly distributed loads by 4.6% and 2.7%, respectively.