With the ever-increasing demand for the miniaturization of polymer capacitors, it is imperative to develop polymer dielectrics with high energy densities, which typically require a combination of high dielectric constant (ε_r) and high breakdown strength (E_b). Currently, incorporating high-ε_r nanofillers into a polymer matrix is considered an effective strategy to enhance the dielectric constant of polymer dielectrics. However, this improvement is often achieved at the expense of reduced breakdown strength. Here, a kind of heterogeneous carbon/silica nanosphere (HCS NS) with abundant internal interfaces is synthesized to enhance the dielectric constant of poly(vinylidene fluoride-hexafluoropropylene) (P(VDF-HFP)) polymer by strengthening interface polarization. Meanwhile, the heterogeneous interfaces also suppress the development of breakdown pathways, thereby preventing excessive deterioration of breakdown strength of the polymer composite. Subsequently, the obtained HCS/P(VDF-HFP) composites are stacked with polyetherimide (PEI) polymer, forming HCS/P(VDF-HFP)-PEI layered composites. Benefiting from the synergistic effect between the high-ε_r HCS/P(VDF-HFP) layer and high-E_b PEI layer, a bilayer composite with 2.5 wt% HCS NSs achieves a significantly enhanced discharge energy density of 10.81 J cm⁻³, which is about 206.3%, 176.1% and 133.5% that of P(VDF-HFP), PEI and the P(VDF-HFP)-PEI composite, along with a high efficiency of 93.8%. It should be noted that the composite retains a high discharge energy density of 9.22 J cm⁻³ and a discharge efficiency of 90.1% even under an elevated temperature of 100 °C. This strategy of combining heterogeneous nanofillers with a layered dielectric structure provides an effective approach for improving the energy storage performance of dielectric composites.