Abstract: The finite element method for transient thermal analysis of composite structure with high-order thermal lamination theory is proposed, and several physical layers of the composite structure is simplified to a single computational layer with temperature continuity condition at the interface of different computational layers. The temperature field in the mid-surface of shell structures are approximated with quadratic interpolation function and assumed that temperature varies in a high-order manner in the thickness direction, so as to improve the computational efficiency of the thermal analysis of laminated composite structures. Compared with numerical results obtained by commercial finite element software, the method proposed is verified by examples of composite structures subjected to concentrated heat flux with both transient temperature field of the cylindrical shell and temperature distribution in thickness direction of plate. Numerical results show that the present transient thermal analysis method for composite structure with high-order thermal lamination theory can accurately simulate the temperature variations both in the plane and in the thickness direction to improve the computational efficiency of thermal analysis as the total number of finite element nodes greatly reduced in the thickness direction. The numerical method proposed could be applied to non-Fourier transient thermal analysis and other extreme practical conditions where temperature varies sharply with both time and space simultaneously.