Anisotropic materials have been widely applied in practical engineering problems of interest. In the paper, the anisotropic heat transfer behaviors are analyzed using the proposed hybrid finite element model with Green’s function kernel. In the established weak integral hybrid functional, the element internal field being approximated with the combination of Green’s function satisfies a priori the governing partial differential equation and the independent frame field is assumed to link the internal field. As a result, the solving linear system of equations with boundary integrals only is obtained and the constructed elements show anisotropic feature. Two numerical examples are given to show the convergence and accuracy of the proposed approach, and the effect of ply angle of orthotropic material principal direction on the temperature distribution is discussed to investigate heat transfer mechanism in anisotropic materials.