Wood has been used in a variety of applications in our daily lives and military industry. Nevertheless, its flammability causes potential fire risks and hazards. Improving the flame retardancy of wood is a challenging task. Herein, a phytic acid-based flame retardant (referred to as AMPA) was synthesized based on supramolecular reactions between melamine and p-amino-benzene sulfonic acid followed by a reaction with phytic acid using deionized water as the solvent. A composite wood was prepared by removing lignin to tailor the unique mesoporous structure of the material, followed by coating AMPA on the surfaces of wood microchannels. The limiting oxygen index of wood has been improved to 52.5% with the addition of 5.6 wt % AMPA. The peak heat release rate for the prepared composite wood was reduced by 81% compared to that for delignified wood, which demonstrates the excellent flame-retardant performance of the prepared composite wood. Furthermore, AMPA and mesoporous structures endow antimicrobial and thermal insulation functions. Hence, this work provides a feasible method for preparing flame-retardant wood-based materials for diversified applications.