Nanocomposites of ferroelectric ceramic filler and polymer matrix show considerable promise as high energy storage dielectric capacitors. However, the influence of microstructure of the ferroelectric filler on the electric energy storage performance in the nanocomposite has not been quantitatively studied, yet it is a key element in understanding the methods employed to improve the performance of capacitors. We demonstrate an innovative strategy to enhance the energy storage density with topological vortex structures in nanocomposites. Using three dimensional phase field calculations, we show that multi-vortex structures can exist in ferroelectric nanowires without charge defects or free charges at the interface between the filler and matrix. The switching behavior of the topological structure (vortex and anti-vortex pair) under external electric field is calculated in nanocylinder wires. The small remnant polarization and very narrow hysteresis loop due to the vortex structure in the nanocomposites can lead to a large enhancement of energy density, as high as 5 J/cm 3 compared to 1-2 J/cm 3 for commercial capacitors, and high energy storage efficiency (over 95%) at a relatively low electric field of 140 MV/m.