High-performance flame-retardant polylactic acid (PLA) bio-composites based on biobased fillers to meet usage requirements represents a promising direction for creating a sustainable world. Although flame retardant PLA composites have been reported extensively, it still remains a huge challenge to develop mechanically robust. The flame retardant PLA composites due to plastication effect of organic flame retardants and poor compatibility of organic fillers with the matrix lead to the severe deterioration in mechanical properties. In this work, a bio-inspired surface manipulation strategy for halloysite nanotubes (HNTs) was proposed via a facile and green self-assembly process. The structure and morphology of bio-inspired HNTs (b-HNTs) proved that biomass nanofillers (PA-NA-Fe) grew well both within the lumen and on the surface of HNTs. The growth of biomass on the inner and outer surfaces of HNTs was inspired from wooden towards enhancing the interface compatibility and imparting multi-properties to PLA biopolymer. Excellent mechanical properties (tensile, thermomechanical and anti-impact mechanical), great fire safety (heat release and smoke emission), thermostability and improved electromagnetic interference shielding effectiveness of this well-designed PLA nanocomposite were realized. The mechanisms of the enhanced performances of the PLA bio-composites by loading b-HNTs were proposed. This work presents a facile and environmentally-friendly bio-inspired modification strategy for HNTs to fabricate high-performance, multi-functional polymer composites, which is also suitable for surface modification of many other nanomaterials, including nanofibers, nanotubes, nanowires, and nanosheets.