The microwave dielectric properties and crystal structures of MgAl2O4 ceramics synthesized using either molten-salt (MA-M) or solid-state reaction (MA-S) methods were characterized in this study. Raman and 27Al solid-state nuclear magnetic resonance spectra indicated that Al3+ cations primarily occupied in tetrahedral sites of the MA-M ceramic. The degree of inversion x, i.e., degree of cation disorder in tetrahedral and octahedral sites, of the MA-M was higher than that of MA-S; such the preferential site occupation of Al3+ cations enhanced the covalency of the MO bonds in the MO4 tetrahedra (M = Mg and Al), leading to a decrease in the lattice parameters. The Q·f of the MA-M fired at 1600 °C was 201,690 GHz, while the MA-S synthesized at 1600 °C exhibited a Q·f of just 85,100 GHz. Based on these results, an intermediate spinel structure with a greater x evidently has a higher Q·f, and therefore the cation distribution is closely related to the Q·f of the ceramic.