This work was focused on the influence of the internal structure of natural rubber (NR)-based core-shell particles on the toughness of polystyrene (PS). Several emulsion polymerization processes were used to control the degree of grafting of the NR phase and the site of polymerization, which determines the final morphology of the prepared composite NR-based particles. PS subinclusions were introduced into the NR core in order to determine their influence on the deformation behaviour of PS. A continuous extrusion process was adapted for the direct feeding of the wet NR-based latexes into the molten PS matrix. Impact testing indicated that core-shell particles based on NR containing a large number of small crosslinked PS subinclusions toughened PS most effectively. A very effective toughening agent is obtained if a hard shell of 25 wt % crosslinked PMMA surrounds the composite rubber particle. Grafting of NR chains during the subinclusion synthesis has to be avoided since a high rubber particle modulus is detrimental for craze nucleation in PS. From the fracture surface morphology the craze nucleating and stabilizing efficiency of composite NR particles having different morphologies or grafting degrees could be deduced.