In order to improve the dielectric properties of existing thermosetting resins, taking advantage of reactive fillers is a simple and feasible option. In this paper, we synthesized a new double epoxycyclohexane double-decker silsesquioxane (DEDDSQ), in which the structure of aliphatic epoxy resin introduced into DDSQ successfully, and the resulting structure of DEDDESQ is confirmed by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR) spectroscopy, and mass spectrometry (MS). Cyanate ester resin was selected as the case study for the application of DEDDSQ as reactive fillers. A CE/E51/DEDDSQ nanocomposite was fabricated by incorporating a small proportion of E51 resin and DEDDSQ into cyanate ester resin to enhance its comprehensive properties. X-ray diffraction (XRD) and energy-dispersive spectroscopy (EDS) analyses demonstrated that DEDDSQ dispersed uniformly within the resin matrix. Dynamic mechanical analysis (DMA) demonstrated that the CE/E51/8.0DEDDSQ nanocomposites exhibit excellent thermal properties. The glass transition temperature (