In this article, a complete structure of corrugated surface is established for heat transfer effects in the presence of uniform magnetic field. A natural convection phenomenon is presented for MHD flow filled in a porous corrugated cavity at various wavelengths and partially heated domain. The governing partial differential equations consist of continuity, momentum and energy equations along with the corrugated conditions at the surface. This system is properly nondimensionalized and then solved via finite element method (FEM). In order to obtain the high resolution near the surface of corrugation, mesh generation is improved at the various portions of the cavity. The flow patterns and temperature distribution within the entire domain of the cavity can be visualized through streamlines and isotherms, respectively. Computational experiment is performed for various values of wavelength number (0 <= n <= 15), Rayleigh number (10(4) <= Ra <= 10(6)), Darcy number (10(-5) <= Da <= 10(-3)), and Hartmann number (10 <= Ha <= 10(3)) to illustrate the effects on streamlines, isotherms, velocities and heat transfer rate. Heat transfer rate is increased due to increase in Rayleigh number and wavelength parameter. Darcy and Hartmann number does not have significant effects on the temperature distribution. (C) 2018 Elsevier Ltd. All rights reserved.