Modified chitosan (CS)-based flame retardants exhibit promising prospects owing to their sustainability, biodegradability, and good charring properties. A series of novel modified-CS bio-based flame retardants (phenylphosphorylated CS (PhPCS) and phenylphosphoramidated CS (PhPNCS)) were prepared by the phosphorylation and phosphoramidation reactions of CS with phenylphosphoryl dichloride and tetraethylenepentamine, respectively. Bio-based PhPCS and PhPNCS exhibited excellent flame retardancy efficiency for poly(lactic acid) (PLA). The limited oxygen index (LOI) values of the PLA/3 wt% PhPCS and PLA/3 wt% PhPNCS biocomposites increased to 29% and 27%, respectively, and they both achieved a V-0 rating during the UL-94 vertical combustion test. However, the mechanical properties of the PLA/PhPCS biocomposites decreased with increasing PhPCS content. The mechanical strengths of the PLA/PhPNCS biocomposites were better than those of the PLA/PhPCS biocomposites owing to the reactive compatibilization of the interface between the amino and carboxyl end groups of the PhPNCS nanoparticles and PLA matrix, respectively.