A series of the densely cross-linked Cyanate Ester Resins (CER)-based composites with 0.01–10wt.% silica, introduced via sol-gel process, were synthesized using dicyanate ester of bisphenol E (DCBE), tetraethoxysilane (TEOS) and γ-aminopropyltrimethoxysilane (APTMS). Their structure, molecular dynamics and properties are investigated by HAADF STEM, EDXS, DMA, DSC, and FTIR and Far-IR spectroscopies. The extremely high “constrained dynamics” effect and the most enhanced thermal, relaxation and elastic properties are revealed for the composites with ultralow silica contents, e.g., up to 0.1wt.%, in the absence of silica nano- or microclusters: increasing Tg by 50°C and dynamic modulus by 60% at 20°C and as much as forty times at 260°C are observed. EDXS analysis including getting the histograms of Si content shows that chemically embedded silica units are distributed quasi-regularly in nanovolumes of amorphous CER matrix in this case. The results obtained lead to conclusion that at ultralow silica contents only subnanometer-sized silica nodes may be generated within the CER network, i.e., the hybrid polymer subnanocomposites are formed. Formation of silica nanoclusters and, especially, their aggregates of hundreds nanometers in size at silica contents of 2–10wt.% results in their negative impact on the matrix properties.