The potential of thermally insulated wood aerogels in energy-efficient engineering is constrained by their mechanical weakness and inadequate environmental stability. Combining minerals with wood aerogels offers promise for enhancing their multifaceted performance. However, fabricating high-performance wood-based aerogels via organic–inorganic assembly remains challenging due to poor uniformity and weak interfacial bonding. Herein, inspired by diatoms, an ultrastrong and flame-retardant biomimetic polymethylsilsesquioxane–wood aerogel (MSQW) is fabricated by combining a nanoscale heterogeneous assembly strategy with sol–gel process to precisely engineer each level of the hierarchy. Meanwhile, the in situ mineralization of amorphous inorganic oligomers firmly welds the organic–inorganic interface, forming a continuous and homogeneous monolithic structure. The resulting MSQW aerogel exhibits ultrahigh stiffness in the axial direction (Young's modulus of 68.73 ± 3.20 MPa) and withstands over 60% strain at 6.97 MPa in the radial direction, recovering its original shape after stress release, due to its unique structural features. Additionally, the aerogel exhibits an excellent combination of properties, including outstanding fire resistance ( peak heat release rate of 91.13 kW/m2), hydrophobicity (water contact angle of 137.3°), and degradability. These advanced properties make MSQW an ideal material for thermal insulation in harsh environments.