Microwave dielectric properties of MgTi1-x(Mn1/3Nb2/3)xO3 (0 ≤ x ≤ 0.05) ceramics were investigated based on their crystal structure characteristics. For the specimens sintered at 1400 °C for 4 h, complete solid solutions with a single phase and an ilmenite structure were obtained for the entire range of compositions. The quality factor (Qf) was dependent on the average Ti-site covalency related to the electronegativity difference and the reduction state of Ti4+. MgTi0.995(Mn1/3Nb2/3)0.005O3 exhibited the highest Qf value of 212,000 GHz owing to the high average covalency obtained from the Rietveld refinement of X-ray Diffraction patterns, high binding energy, and small full width at half maximum of Ti 2p peaks, as confirmed by X-ray Photoelectron Spectroscopy of MgTiO3 –based ceramics. The temperature coefficients of the resonant frequency (TCF) of MgTiO3-based ceramics were dependent on the degree of average oxygen octahedral distortion of the ilmenite structure. The dielectric constant (K) was affected by the theoretical dielectric polarizability of the constituent ions of sintered specimens. Excellent microwave dielectric properties were obtained for MgTi0.995(Mn1/3Nb2/3)0.005O3; K = 18.05, Qf = 212,000 GHz, TCF = − 37.04 ppm/°C. The microwave dielectric properties were improved by substituting (Mn1/3Nb2/3)4+ for Ti4+ in MgTiO3-based ceramics.