Abstract: Based on the energy variational principle, the governing differential equations and their corresponding boundary conditions of a box girder are derived, in which three different displacement functions are employed to describe the warping amplitudes of bottom slab, top slab and flange slab due to the shear lag, respectively. The cross-section axial force is regarded to be in a self-equilibrium condition and there exists the shear deformation in the web. The initial-value solutions of the equations under a uniformly distributed load are obtained. A transfer matrix method for shear lag analysis of a non-uniform continuous box girder is put forward. The field transfer matrix and point matrix are derived, and the inner force, stress and deflection of a non-uniform continuous box girder can be recursively calculated. The numerical results are compared with those from the model test or existed documents, which verifies the accuracy and efficiency of the method given in the paper.