There is an urgent demand for polymer dielectrics in the rapidly growing fields of electric vehicles and energy exploration. However, the existing polymer dielectrics suffer from poor energy density due to the decrease of breakdown strength at elevated temperatures, which limits their widespread application. Ultralow content inorganic fillers (< 1 vol.%) with appropriate size have been reported to enhance the polarization of polymer matrix, while their influence on breakdown still lack attention. In this work, we developed the dilute polyetherimide (PEI)-Al₂O₃ nanocomposites with different filler size (5, 20, and 80 nm) and studied the size effect of nanofillers on the breakdown resistance and energy storage performances of nanocomposite dielectrics. Based on the results of multiscale simulations and tests, the dilute fillers with smaller size (5 nm) exhibit more remarkable enhancement on charge trapping and mechanical strengthening of polymer matrix, and thus yielding higher breakdown strength and a discharged energy density of 4.69 J·cm⁻³ (150 °C) and 2.56 J·cm⁻³ (200 °C) with a high efficiency of 90%. A long charge–discharge cycling stability up to 10⁵ cycles was also achieved at 150 °C.