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In this paper, we consider a coupled system of equations that describes simplified magnetohydrodynamics (MHD) problem in perforated domains. We construct a fine grid that resolves the perforations on the grid level in order to use a traditional approximation. For the solution on the fine grid, we construct approximation using the mixed finite element method. To reduce the size of the fine grid system, we will develop a Mixed Generalized Multiscale Finite Element Method (Mixed GMsFEM). The method differs from existing approaches and requires some modifications to represent the flow and magnetic fields. Numerical results are presented for a two-dimensional model problem in perforated domains. This model problem is a special case for the general 3D problem. We study the influence of the number of multiscale basis functions on the accuracy of the method and show that the proposed method provides a good accuracy with few basis functions.