Carbon aerogels (CAs) had been well applied in extreme condition thermal insulation, but achieving a balance between mechanical robustness and thermal insulation remains challenging. We present a novel strategy to fabricate carbon aerogels with tunable mechanical properties and thermal insulation properties by tailoring their skeleton architecture via molecular assembly. Carbon precursor aerogel with thick neck particle packing structure was obtained by strong hydrogen-bonding-induced self-assembly between polyurethane-urea oligomer (PUU) and phenolic resin (PF), and carbon aerogel retained robust interparticle connections after pyrolysis, resulting in excellent mechanical properties. The presence of PUU leads to denser packing of resin molecules, promotes graphitization of the carbon and formation of nanocrystalline structures at 1400 °C, resulting in optimized compression modulus and strength. The closed pore structure of carbon skeleton was further studied by Small-Angle X-ray Scattering (SAXS), while moderate pore width (0.4–0.6 nm) optimizes the balance between strength (110 MPa) and thermal conductivity (0.30 W/(m·K)). This work demonstrates that molecular-level assembly combined with pyrolysis control enables precise tuning of carbon aerogel structures and properties, providing new insights for high-temperature thermal insulation applications.