This paper presents a robust numerical solution to the electromagnetic scattering problem involving multiple multi-layered cavities in both transverse magnetic and electric polarizations. A transparent boundary condition is introduced at the open aperture of the cavity to transform the problem from an unbounded domain into that of bounded cavities. By employing Fourier series expansion of the solution, we reduce the original boundary value problem to a two-point boundary value problem, represented as an ordinary differential equation for the Fourier coefficients. The analytical derivation of the connection formula for the solution enables us to construct a small-scale system that includes solely the Fourier coefficients on the aperture, streamlining the solving process. Furthermore, we propose accurate numerical quadrature formulas designed to efficiently handle the weakly singular integrals that arise in the transparent boundary conditions. To demonstrate the effectiveness and versatility of our proposed method, a series of numerical experiments are conducted.

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