According to concrete box beam which flanges depth varying along the orientation of cross section, using variational principle of potential energy, new analysis method of shear lag is proposed for single cell concrete box beam. For simply supported girders and cantilever girders, general analysis of varying flange-depths influence on positive and negative shear-lag effect and deflection have be done. It's shown that varying flange-depths have influence both on sectional stress and deflection. Considering the varying flange-depths have effect on the calculation results of up to 15%.