A bio-based intumescent flame retardant (IFR) was designed and synthesized by employing a simple and environment-friendly strategy. Via electrostatic interaction, chitosan (CS) and amino trimethylphosphonic acid (ATMP) as organic shells are deposited on the inorganic core of ammonium polyphosphate (APP) to form the core–shell flame retardant ([email protected]@ATMP). Then, agar (AG) is used as a charring agent candidate that combines with [email protected]@ATMP to fabricate a bio-based IFR. The application of [email protected]@ATMP and AG in polylactic acid (PLA) is effective in improving its flame retardancy and anti-dripping properties. The PLA composite including 20 wt% [email protected]@ATMP/AG ([email protected]@ATMP:AG = 3:1) can achieve the optimal flame-retardant effect and a UL-94 V-0 rating with a slight melt-dripping phenomenon. Furthermore, the peak heat release rate and total heat release significantly decrease in the cone calorimetric tests contrasted with those of pure PLA. The flame-retardant mechanism of [email protected]@ATMP/AG is revealed by analyzing the pyrolysis gaseous products during the thermal decomposition and the morphology and structure of char residues. This work provides a facile and sustainable route to construct bio-based polymer composites with excellent fire-safety properties.