Polymer nanocomposites incorporated with high-dielectric-constant nanoparticles are widely studied as the dielectric materials for high-energy-density electrostatic capacitors. However, the associated concerns of the embedded nanoparticles such as local electric field distortion and high leakage current limit the substantial improvement of energy density. In this work, a novel design of hierarchically-structured nanofillers is demonstrated, which show remarkable advantages over conventional high-dielectric-constant nanoparticles for polymer nanocomposites. These hierarchical nanostructures are prepared by covalently tethering the barium titanate (BT) nanoparticles on the basal plane of the two-dimensional boron nitride nanosheets. The grafting density of BT in the hierarchical nanostructures is adjustable such that its dielectric properties can be tuned, and the capacitive energy storage performance of the nanocomposites can be optimized. Both the experimental results and computational simulations prove that the hierarchically-structured nanofillers can effectively suppress the local field distortion and reduce leakage current. The resulting polymer nanocomposite exhibits a high discharged energy density which is 137% greater than that of a conventional nanocomposite with the same content of freely dispersed BT nanoparticles, in addition to a much improved charge–discharge efficiency. The proposed hierarchically-structured nanofillers shed light on the design of polymer nanocomposites with high energy density and high charge–discharge efficiency.