To avoid potential life and economic loss, structural health monitoring has become increasingly important for bridge systems. As a key component of structural health monitoring, structural system identification (SSI) tries to identify the structural parameters through the measured response. However, due to the ill-posedness of inverse analysis, the estimation of parameters is greatly affected by measurement errors. To alleviate the adverse effect of errors, the relations among the displacements in beam structures (for instance bridges), compatibility conditions, are derived analytically via a symbolical approach. Then a set of compatible displacements is obtained by an optimization procedure that finds the closest compatible deformation shape to the measured one. The final estimations of the parameters are obtained by providing the compatible displacements to SSI. The proposed method is validated by the numerical simulations on a simply supported bridge and on a continuous bridge.