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Nanocomposites of cyanate ester resin (CER) filled with three different reactive amino-functionalized polyhedral oligomeric silsesquioxane (POSS) were synthesized and characterized. The addition of a small quantity (0.1 wt.%) of amino-POSS chemically grafted to the CER network led to the increasing thermal stability of the CER matrix by 12–15 °C, depending on the type of amino-POSS. A significant increase of the glass transition temperature, <i>T</i>_g (DSC data), and the temperature of α relaxation, <i>T</i>_α (DMTA data), by 45–55 °C of the CER matrix with loading of nanofillers was evidenced. CER/POSS films exhibited a higher storage modulus than that of neat CER in the temperature range investigated. It was evidenced that CER/aminopropylisobutyl (APIB)-POSS, CER/<i>N</i>-phenylaminopropyl (<i>N</i>PAP)-POSS, and CER/aminoethyl aminopropylisobutyl (AEAPIB)-POSS nanocomposites induced a more homogenous α relaxation phenomenon with higher <i>T_α</i> values and an enhanced nanocomposite elastic behavior. The value of the storage modulus, <i>E</i>′, at 25 °C increased from 2.72 GPa for the pure CER matrix to 2.99–3.24 GPa for the nanocomposites with amino-functionalized POSS nanoparticles. Furthermore, CER/amino-POSS nanocomposites possessed a higher specific surface area, gas permeability (CO₂, He), and diffusion coefficients (CO₂) values than those for neat CER, due to an increasing free volume of the nanocomposites studied that is very important for their gas transport properties. Permeability grew by about 2 (He) and 3.5–4 times (CO₂), respectively, and the diffusion coefficient of CO₂ increased approximately twice for CER/amino-POSS nanocomposites in comparison with the neat CER network. The efficiency of amino-functionalized POSS in improving the thermal and transport properties of the CER/amino-POSS nanocomposites increased in a raw of reactive POSS containing one primary (APIB-POSS) < eight secondary (<i>N</i>PAP-POSS) < one secondary and one primary (AEAPIB-POSS) amino groups. APIB-POSS had the least strongly pronounced effect, since it could form covalent bonds with the CER network only by a reaction of one -NH₂ group, while AEAPIB-POSS displayed the most highly marked effect, since it could easily be incorporated into the CER network via a reaction of –NH₂ and –NH– groups with –O–C≡N groups from CER.