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We present a non-traditional finite element method for the electromagnetic scattering of the partly covered groove filled with multiple media. The non-local boundary condition is introduced to make the unbounded scattering into a bounded domain problem. Non-body-fitted mesh is applied to save the cost of discretizing groove domain greatly. In addition, the level set functions are utilized to describe complex media interfaces and boundaries. Numerical tests demonstrate the effectiveness and second-order convergence rate of the proposed method.