Polymer nanocomposites have attracted broad attention in the area of dielectric and energy storage. However, the electrical and chemical performance mismatch between inorganic nanoparticles and polymer leads to interfacial incompatibility. In this study, phosphonic acid molecules with different functional ligands were introduced to the surface of BaTiO3 (BT) nanoparticles to tune their surface properties and tailor the host–guest interaction between BT and poly(vinylideneflyoride-co-hexafluroro propylene) (P(VDF-HFP)). The dielectric properties and electrical energy storage capability of the nanocomposites were recorded by broadband dielectric spectroscopy and electric displacement measurements, respectively. The influence of the ligand length and polarity on the dielectric properties and electrical energy storage of the nanocomposites was documented. The nanocomposite with 5 vol% 2,3,4,5,6-pentafluorobenzyl phosphonic acid (PFBPA)-modified BT had the highest energy density of 12.8 J cm−3 at 400 MV m−1, i.e., a 187% enhancement in the electrical energy storage capability over the pure P(VDF-HFP). This enhancement can be attributed to the strong electron-withdrawing effect of the pentafluorobenzyl group of PFBPA, which changed the electronic nature of the polymer–particle interface. On the other hand, PFBPA improves the compatibility of the host–guest interface in the nanocomposites and decreases the electrical mismatch of the interface. These results provide new insights into the design and preparation of high-performance dielectric nanocomposites.