Epoxy-based silsesquioxane (EOVS) was successfully oxidized from octavinyl silsesquioxane (OVS) and then prepared the E51/BADCy/EOVS nanocomposites with epoxy resin and cyanate ester. With EOVS additions, a lower value of dielectric constant was achieved due to the increased free volume. The positron annihilation lifetime spectroscopy (PALS) demonstrated more nanocavity introduced by POSS increased the free volume of the system, and the crosslinking density calculated from DMA was combined to determine the spatial structure of molecular chains in nanocomposites. Subsequently, the internal microstructure of materials and the types of dipoles were confirmed by Fourier transform infrared spectroscopy (FTIR) and electron paramagnetic resonance spectroscopy (EPR), and the effect of various dipoles on the dielectric loss was fully discussed. Surprisingly, the dielectric constant and dielectric loss even decreased to 2.0 and 0.0036 (1 MHz), which suggested E51/BADCy/EOVS nanocomposites are promising candidates in the aspect of microelectronics industry.