The paper focuses on the numerical study of electromagnetic scattering from twodimensional (2D) large partly covered cavities, which is described by the Helmholtz equation with a nonlocal boundary condition on the aperture. The classical five-point finite difference method is applied for the discretization of the Helmholtz equation and a linear approximation is used for the nonlocal boundary condition. We prove the existence and uniqueness of the numerical solution when the medium in the cavity is y-direction layered or the number of the mesh points on the aperture is large enough. The fast algorithm proposed in [2] for open cavity models is extended to solving the partly covered cavity problem with (vertically) layered media. A preconditioned Krylov subspace method is proposed to solve the partly covered cavity problem with a general medium, in which a layered medium model is used as a preconditioner of the general model. Numerical results for several types of partly covered cavities with different wave numbers are reported and compared with those by ILU-type preconditioning algorithms. Our numerical experiments show that the proposed preconditioning algorithm is more efficient for partly covered cavity problems, particularly with large wave numbers.