The applications of silica aerogels are restricted due to their intrinsic fragile property. Polymerization of di-isocyanates can be templated onto the mesoporous surface of the –NH2 group modified silica clusters, resulting in the conformal crosslinked coating on surface of silica clusters. Aminopropyltriethoxysilane (APTES), as the silica co-precursor and amine group modification agent, is involved containing tetramethyl orthosilicate (TMOS) silica precursor, while hexamethylene diisocyanate (HDI) is incorporated as the polymer crosslinking agent. The effects of different amounts of APTES on the physicochemical properties of the resulting crosslinked aerogels are investigated. The results show that the optimized APTES/TMOS volume ratio can be determined at 0.5:1. The resulting optimal crosslinked silica aerogel possesses large BET specific surface area of 150.9 m2/g, low thermal conductivity of 0.037 W/(m·K), and the Young's modulus is as large as 18 MPa under strain of 4.2%, much higher than that in the previously published works. The polymerization reaction mechanism forming the polyurethane chains has also been proposed. In addition, the interactions between silica clusters and polymer chains are studied by molecular mechanics and molecular dynamics. The interactions are mainly dependent on non-bonding energy, and the electrostatic energy has decisive impact on the combination of silica clusters and polymer chains. The density field of C, H, N, O, and Si elements overlaps with each other, indicating that the polymer crosslinked silica aerogel maintains typical three-dimensional porous structure. The N element enriches in the region between silica clusters, further verifying the formation –CONH–(CH2)6–CONH- polyurethane chains, which is actually responsible for the much enhanced mechanical property.