Low-flammability freeze-dried cellulose nanofibril (CNF)/sodium montmorillonite (MMT) aerogels with improved mechanical properties were fabricated via a facile cross-linking of boric acid (BA) and melamine-formaldehyde (MF) resins. Scanning electron microscopy analysis showed that BA cross-linking reduced the interspacing of layered CNF/MMT aerogels whereas introduction of MF formed polymeric fibrils that connected the layers. These changes on microstructures resulted in the improvement on compressive mechanical properties of the cross-linked aerogels. Moreover, the boron (B)/nitrogen (N) containing flame retardant cross-linkers greatly increased the limiting oxygen index values that could reach 85% and leveled the UL-94 rating from no rating to V-0. Cone calorimetric results suggested that BA and MF induced a synergistic effect on the flame retardant properties of the CNF/MMT aerogels. However, the thermal conductivity was little affected because pore structure and size was not substantially modified. This simple approach fabricated highly flame-resistant and mechanically strong CNF-based aerogels that could be used in various engineering fields