In this paper, the structural health monitoring (SHM) benchmark problem of the Canton tower is studied. Based on the field monitoring data from the 20 accelerometers deployed on the tower, some modal frequencies and mode shapes at measured degrees of freedom of the tower are identified. Then, these identified incomplete modal data are used to update the reduced finite element (FE) model of the tower by a novel algorithm. The proposed algorithm avoids the problem of subjective selection of updated parameters and directly updates model stiffness matrix without model reduction or modal expansion approach. Only the eigenvalues and eigenvectors of the normal finite element models corresponding to the measured modes are needed in the computation procedures. The updated model not only possesses the measured modal frequencies and mode shapes but also preserves the modal frequencies and modes shapes in their normal values for the unobserved modes. Updating results including the natural frequencies and mode shapes are compared with the experimental ones to evaluate the proposed algorithm. Also, dynamic responses estimated from the updated FE model using remote senor locations are compared with the measurement ones to validate the convergence of the updated model.