In this work, the effect of magnetic polaritons (MPs) inside the SiC grating microstructures on near-field radiative transfer is theoretically studied. Fluctuational electrodynamics that incorporates scattering matrix theory with rigorous coupled-wave analysis is employed to calculate the spectral heat flux between two SiC deep gratings. The results are compared with effective medium theory and proximity approximation method. Besides the well-known coupled surface phonon polaritons (SPhP), MPs can also greatly affect the spectral heat flux. Confined magnetic field inside the SiC grating grooves, contour plot of transmission coefficient and the prediction by an inductor-capacitor circuit model are used to elucidate the effect of MP excited within the grating grooves on the near-field radiative transfer. It shows that, compared to the near-field heat flux between two SiC plates, the one between SiC gratings can be enhanced with large vacuum gaps, while suppressed at small vacuum gap distances. The effects of misalignments, geometrical parameters and vacuum gap distances on both SPhP and MP are investigated as well. (C) 2017 Elsevier Ltd. All rights reserved.