Some efforts have been made to strengthen the environment friendly natural fiber-reinforced polylactide composite (NFPC), but common approaches impair its ductility. This paper successfully synthesized the rigid-soft core-shell nanoparticles which are feasible to simultaneously improve the strength and toughness of NFPC. The core-shell structure was molecularly designed to act the nano-silica and poly (butyl acrylate) rubber as rigid inner core and soft outer shell, respectively. Furthermore, the devised active functional groups at the end of core-shell filler also interact with polylactide (PLA) matrix to form strong interface. The effect of core-shell nanoparticle on crystalline, thermal and mechanical properties of NFPC was investigated. The results showed that the core-shell nanofiller can facilitate to form the more complete crystalline grain of PLA matrix and the thermal stability improvement of NFPC. More attractively, the addition of the rigid-soft core-shell nanoparticle enhanced the strength and stiffness of NFPC without sacrificing its elongation at break. Finally, the toughness improvement mechanisms and synergistic effect of core-shell nanoparticles were illustrated via field emission scanning electron microscope. It indicates that the micro-cracks, shear band and fibration of the matrix induced by the core-shell filler are the main causes of toughness improvement.