Microwave‐sintering (MWS) technique was employed to fabricate dense (Ba0.4Sr0.6)TiO3 (BST) ceramics. With respect to the high dielectric loss at room temperature, induced by the formation of oxygen defects during the MWS under vacuum atmosphere (−60 kPa), the as‐sintered samples were thermally annealed in air to reduce tanδ and recover the insulating performance. Accompanied by the decreased tanδ, the energy storage properties for annealed MWS BST were optimized, with increasing energy density (γ) from 0.77 to 1.15 J/cm3 and energy efficiency (η) from 60% to 82%. The lower oxygen vacancy concentrations were believed to account for the enhanced insulating characteristics of grain boundaries and contribute to the improved properties after annealing. Electrical characterization of grain and grain boundary by impedance spectroscopy demonstrated that the annealing preferentially modified the grain boundary. In addition, resistances extracted from the high temperature impedance analysis were found to be inadequate for evaluating the electrical characteristics of materials affected by extrinsic mechanisms, such as the interfacial polarization. For comparison, annealing effect on energy storage properties were also discussed for conventionally sintered BST.