Bio-based aerogel is a functionalized nanoporous material with environmentally friendly, high surface area, ultra-low density, high porosity, and low thermal conductivity, making it suitable for various applications such as energy-saving buildings, electronic information, separation, adsorption, catalysis, biomedicine, and others. However, the current bio-based chitosan aerogel still faces great challenges in reaching multifunctional improvement to address its intrinsic shortcomings. Herein, we propose a new approach depending upon supramolecular interactions for constructing chitosan/bacterial cellulose aerogels that simultaneously possess superior moisture resistance/fatigue, anti-thermal-shock, and flame retardancy. Specifically, the aerogels demonstrate remarkable characteristics, namely high strength (self-standing itself weight beyond 10,676 times), low thermal conductivity (lowest to 22mWm-1K-1 under normal pressure and room temperature), and excellent fatigue resistance (almost negligible permanent deformation at 1% strain even undergoing compressive cycles up to 10,000 times). On the other hand, the aerogels display exceptional moisture resistance with superhydrophobicity (moisture absorption rate <0.88% for 160h at 70°C and 85% relative humidity), excellent thermal shock property (withstand cold-hot shock up to 200cycles with rapid temperature changes between -30°C and 60°C), and remarkable fire retardancy (swiftly self-extinguishing in 0.6s). Additionally, the compressive stress increases to 0.223MPa at 3% strain after hydrophobic treatment, representing a 27% enhancement in mechanical robustness. Further, the mechanism responsible for microstructural evolution has been also established in different strain conditions. This work may provide rich possibilities for developing multifunctional bio-based aerogel for energy-saving buildings.