The influence of manganese substitution on the sintering and dielectric properties of Mg3B2O6 (MBO) was studied, and the detailed mechanism of variation was discussed using density functional theory calculations. The characterization method involved a network analyser, differential–thermal analyses, thermomechanical analyses, X‐ray diffraction, and scanning electron microscopy. Manganese substitution formed a two‐phase system (MBO and Mg2B2O5), improved the dielectric property, densified the microstructure, lowered the activation energy, decreased the crystallite size, modified the band structure property, and strengthened the covalency of MgO6 octahedron. The 7% mole substitution of manganese to magnesium improved the dielectric properties of MBO to 7.06 for εr and 61 100 GHz at 15 GHz for Q × f, −54.8 ppm/°C for τf. The intrinsic densification temperature decreased from 1350 to 1175°C with 97.7% relative density.