This paper proposes a new modeling method for joints in mechanical structures in order to reduce the errors in eigenvalue analysis due to joint modeling. The new modeling method uses both a stiffness influence method and a condensation method to obtain the dynamic characteristic matrix of the joint region. It also employs the displacement and reaction of finely modeled finite element analysis in the calculation of stiffness influence coefficients. In order to check the validity of the proposed method, natural frequencies and mode shapes of a simple structure with a bolted joint are investigated by the proposed method and by experiments. The eigenvalue analysis using the proposed method shows more accurate results than that using rigid joints modeling, when the natural frequencies are compared with the experimental results. In addition, the differences between the natural frequencies obtained by the proposed method and those by the rigid joints modeling are notable in the modes where the joint has elastic deformation.