The paper proposes an identification method of the dynamic stiffness matrix of a bearing joint region on the basis of theoretical analysis and experiments. The author deduces an identification model of the dynamic stiffness matrix from the synthetic substructure method. The dynamic stiffness matrix of the bearing joint region can be identified by measuring the matrix of frequency response function (FRFs) of the substructure (axle) and whole structure (assembly of the axle, bearing, and bearing housing) in different positions. Considering difficulty in measuring angular displacement, applying moment, and directly measuring relevant FRFs of rotational degree of freedom, the author employs an accurately calibrated finite element model of the unconstrained structure for indirect estimation. With experiments and simulation analysis, FRFs related with translational degree of freedom, which is estimated through the finite element model, agrees with experimental results, and there is very high reliability in the identified dynamic stiffness matrix of the bearing joint region.