The high-efficient and accurate analysis of anisotropic composite media weakened by a large amount of holes or cuts is still a great challenge in practical composite engineering. In this work, specially-proposed polygonal finite element enclosing an arbitrarily oriented elliptical hole in general anisotropic composite media is formulated for thermal analysis in the framework of hybrid finite element theory. Two independent temperature field approximations are defined for the present special element: Intra-element temperature field and element frame temperature field. The former defined inside the element is written in the form of truncated summation of the weighted special fundamental solutions, which are derived using the Stroh complex theory and conformal mapping whilst the latter is implemented by the conventional shape function interpolation. Then the hybrid variational functional is employed to combine them together to generate an element stiffness equation with respect to nodal temperature and an optional relationship between the interpolation coefficients. The element stiffness matrix is symmetric and involves element boundary integrals only. Compared to the traditional finite element, the distinctive element-boundary-integral and enclosed-elliptical-hole features make the present element significantly improve the meshing effort around an elliptical hole by reducing the number of elements and decreasing the meshing difficulty, and more importantly, effectively capture the critical variation of physical fields around the elliptical hole without locally-refined meshes. Moreover, the present special element can be incorporated directly into the conventional finite element system without any difficulty for extensive analysis. Finally, several typical examples are simulated by the present special elements to demonstrate their effectiveness.