A one-dimensional high-order dynamic model for single-box twin-cell box girders is presented together with the pattern recognition algorithm. The model takes into account the deformable cross-section and can accurately predict its 3D dynamic behaviors. The cross-section deformation is captured by basis functions satisfying displacement continuity condition, which is essential to construct the initial model formulation based on the Hamilton principle. The axial variation patterns of generalized coordinates are decoupled by solving the eigenvalue problem. On this basis, the combinations of basis functions are obtained to bring out cross-section deformation. The cross-section deformation, hierarchically organized and physically meaningful, are used to update the basis functions in the reconstructed high-order model. Numerical analysis has verified the accuracy and applicability of the reconstructed one-dimensional high-order model.