Poly(lactic acid) (PLA) is a widely reusable polymer, but its practical applications are greatly constrained by low toughness and poor crystallinity. In this study, the modified cellulose nanocrystal (CNC) was designed as a reinforcement through surface copolymerization of caprolactone (CL) and allyl caprolactone (ACL) to enhance the properties of PLA. The surface molecular engineering of reactive core-shell nanofillers (allyl polycaprolactone-grafted CNC, or CNC-g-APCL) effectively improved the interfacial compatibility between PLA and CNC through a straightforward in situ reactive extrusion process. The presence of elastic polycaprolactone (PCL) and allyl polycaprolactone (APCL) rendered good energy dissipation as evidenced by the improved toughness and elongation at break of the PLA/CNC hybrid composites. More importantly, the integrated CNC composite presented an extremely high crystallinity of 45.1 %, which is top-ranking among all reported studies on PLA/CNC nanocomposites. In summary, this research introduces an innovative method for designing nanocomposites with improved interfacial compatibility between the matrix and components by grafting copolymerization and reactive extrusion, providing a universal solution to the mechanical and crystalline deficiencies often observed in biodegradable polymers.