As the third generation of novel aerogels, cellulose aerogels exhibit broad applications in various fields, indicating its great development potential. Whereas the flammability and poor mechanical performance of cellulose aerogel restrict its practical application. Herein, a kind of flame retarded and reinforced aerogel was fabricated using cellulose nanofibrils (CNFs) and sodium alginate (SA) as compound matrix (CA) based on double cross-linking strategy. Boric acid (BA)/Ca²⁺ were used as synchronous flame retardants and cross-linking agents. FT-IR spectra of compound aerogels confirmed the occurrence of cross-linking reaction. Due to the formation of interpenetrating networks, especially the specific eggbox structure formed by the cross-linking between Ca²⁺ and SA, the double cross-linked specimen (CA/Ca/BA-3) exhibited decreased pore size and porosity, also resulting in the improved mechanical performance. The double cross-linked aerogel also exhibited excellent flame-resistant properties. The limiting oxygen index (LOI) of CA/Ca/BA-3 increased from 20.4 to 35.6%, and vertical combustion test (UL-94) rating reached V-0 level. The results of microcalorimetry showed that the maximum heat release rate (pHRR) and total heat release (THR) of CA/Ca/BA-3 decreased by 48% and 62% in comparison with control specimen (CS), respectively. The analysis of carbon residues showed that both condensed phase and gaseous phase flame-retardant mechanisms existed, and synergistic effect between BA and CaCO₃ occurred during combustion. Moreover, the very low thermal conductivity of compound aerogels permitted their application as heat insulation materials. This investigation is helpful to promote the functionalization of cellulose aerogel while taking into account the increasingly stringent environmental requirements.