High dielectric constant (εr) inorganic nanoparticles reinforced dielectric polymer nanocomposites have been intensively investigated for energy storage applications in current electrical and electronic systems. Although the incorporation of high-εr inorganic nanoparticles can improve the εr of the composites to a certain extent, it will also greatly reduce the overall breakdown strength (Eb) of the materials, which ultimately hinders the effective improvement of the energy storage density of the composites. In this paper, an approach is developed to modify high-εr BaTiO3 (BTO) nanoparticles with polyimide (PI) polymer shells (PI@BTO) through an in-situ polymerization process in the polyetherimide (PEI)-based nanocomposites. The constructed PI shell improves the compatibility of the inorganic/organic interface, resulting in a uniform dispersion of nanoparticles in the PEI matrix. In particular, the spontaneous electrostatic interaction between polymer chains in the PI shell and PEI matrix enables an increased Eb of the PEI/PI@BTO nanocomposite over the pure PEI, which leads to a high energy storage density (Ue) of 6.2 J/cm3 and a high charge-discharge efficiency (η) above 80% in the PEI nanocomposites, with an enhancement of 150% over pure PEI. In this paper, a convenient and efficient interfacial modification technique is provided for the development of flexible high energy storage density polymer/inorganic nanoparticle composites for dielectric and energy storage applications.