The Hertzian displacement assumption is widely used in analyzing the contact problems of non-uniform elastic bodies. It is essential to account for the support conditions of the elastic body as they significantly influence the contact stiffness and distribution of contact pressure. To address this, the deformation of beam structures is integrated into the Hertzian displacement assumption, which leads to the development of an extended contact mechanics model suitable for the elastic bodies of a beam structure which can be non-uniform and with functionally graded coatings. The problem is solved by using a numerical method based on the Gauss–Chebyshev quadrature for the singular integral equation of Cauchy type. In the contact problems of the doubly simply supported (SS-SS) and cantilever beams, the contact pressure and contact stiffness in conjunction with the interactions between the indentation and contact bodies are discussed. An in-depth study on the coupling effects between the structural deformation and functionally graded coatings is presented.