In the most recent electronic and electric sectors, ceramic-polymer nanocomposites with high dielectric permittivity and energy density are gaining popularity. However, the main obstacle to improving the energy density in flexible nanocomposites, besides the size and morphology of the ceramic filler, is the low interfacial compatibility between the ceramic and the polymer. This paper presents an alternative solution to improve the dielectric permittivity and energy storage properties for electronic applications. Here, the poly(vinylidene fluoride-hexafluoropropylene) (PVDF-HFP) matrix is filled with surface-modified BaTi0.89Sn0.11O3/polydopamine nanoparticles (BTS11) nanoparticles, which is known for exhibiting multiphase transitions and reaching a maximum dielectric permittivity at room temperature. BTS11 nanoparticles were synthesized by a sol-gel/hydrothermal method at 180 °C and then functionalized by polydopamine (PDA). As a result, the nanocomposites exhibit dielectric permittivity (εr) of 46 and a low loss tangent (tan δ) of 0.017 at 1 kHz at a relatively low weight fraction of 20 wt% of BTS11@PDA. This is approximately 5 times higher than the pure PVDF-HFP polymer and advantageous for energy storage density in nanocomposites. The recovered energy storage for our composites reaches 134 mJ cm-3 at an electric field of 450 kV cm-1 with a high efficiency of 73%. Incorporating PDA-modified BTS11 particles into the PVDF-HFP matrix demonstrates highly piezo-active regions associated with BTS11 particles, significantly enhancing functional properties in the polymer nanocomposites.