Developing clay-based aerogel composites with integrated high strength, low thermal conductivity, and hydrophobicity remains a great challenge. Here, binary-network structured montmorillonite/silica composite aerogels (CSACs) with improved mechanical strength were engineered via the in-situ growth of silica networks in the montmorillonite aerogel scaffolds. Tunable density (0.065–0.149 cm3/g) and porosity (92.3–96.2%) can be achieved by different silica sol volumes (silica network content). The filled silica networks endow aerogels with a complete transition from hydrophilicity to hydrophobicity, showing high water contact angles of >130° and extremely low water absorption of 9.9%. CSACs show enhanced stress transfer and load-bearing capacity, with 2.6 and 4.4 times increased compressive modulus and strength compared to pure montmorillonite aerogel scaffolds. Moreover, a noteworthy reduction in thermal conductivity (0.041 to 0.034 W/(m∙K)), the decreased maximum thermal decomposition rates (dw/dt), increased temperature at the maximum decomposition rates (Tmax), and residues confirm the improved thermal insulation and thermal stability of CSACs, respectively. This research provides new insights into the design of efficient thermal insulation materials for diverse energy-saving scenarios that require excellent combined properties.