In this work, Mn-doped 0.9BaTiO3-0.1Bi(Mg2/3Nb1/3)O3 ceramics were prepared by the conventional solid state reaction method, and the effect of defect dipoles on energy storage properties of lead free relaxor ferroelectric BaTiO3-based ceramics was studied. The crystal structure, dielectric properties, and energy storage properties were explored in detail. It was found that polarization hysteresis (P-E) loops of 0.9BaTiO3-0.1Bi(Mg2/3Nb1/3)O3-x wt. % MnCO3 (0.2–0.5) ceramics took on high maximum polarization (Pmax) and low remanent polarization (Pr). Meanwhile, recoverable energy density (Wrec) and energy conversion efficiency (η) were obviously enhanced by inducing defect dipoles into BaTiO3-Bi(Mg2/3Nb1/3)O3 relaxor ferroelectrics. The 0.9BaTiO3-0.1Bi(Mg2/3Nb1/3)O3-0.3 wt. % MnCO3 ceramic was found to exhibit good energy storage properties with a Wrec of about 1.70 J/cm3 and a η ∼ 90% under an electric field of 210 kV/cm. The breakdown electric field and Wrec of BaTiO3-based materials were significantly increased in the present work, and they might be good candidates for high power energy storage applications.