The development of bio-based flame retardants has garnered significant attention, however, significant challenges remain in achieving efficient flame retardancy and eco-friendly preparation methods. Herein, we propose a facile, atomic-efficient, and eco-friendly strategy for synthesizing a trinity chitosan-based flame retardant, phosphite-protonated chitosan (PCS). The chemical structure was systematically analyzed and the impact of varying degrees of protonation on the dissolution behavior and rheological properties were investigated. Benefiting from the promotion of dehydration and carbonization facilitated by phosphite groups, PCS exhibits high intrinsic flame retardancy with an LOI value of 80.7 %. Moreover, its favorable rheological and film-forming properties make it well-suited for easy application as a multifunctional coating in fabric finishing through blade coating processes. The finished cotton and polyester/cotton blended fabrics exhibit excellent flame retardancy, as evidenced by increased LOI values, successful passage of vertical burning tests, reductions of up to 65.0 % and 50.3 % in pHRR and THR values, respectively. Additionally, PCS imparts superior antibacterial properties to the fabrics, achieving a 99.99 % antibacterial rate against both E. coli and S. aureus. This study introduces a straightforward and atom-economical approach for preparing highly efficient chitosan-based flame retardants, along with the development of a transparent, green, and efficacious multifunctional coating system on textiles.