Submicron polybutadiene particles were prepared using four different methods: one-step batch emulsion polymerization, pressure agglomeration, acid agglomeration, and polymer latex agglomeration. Core-shell elastomers were synthesized by grafting styrene and methyl methacrylate on polybutadiene particles. Transparent methacrylate-acrylonitrile-butadiene-styrene resin was prepared by blending the elastomers with methacrylate-styrene-acrylonitrile matrix resin synthesized by bulk polymerization. The effects of the construction method of submicron rubber particles on core-shell elastomer structure and composite properties were investigated. Additionally, the relationship between the rubber phase structure and composite properties was studied. The obtained results showed that the construction method significantly affected the size distribution and morphology of the submicron rubber particles. The rubber particles prepared by one-step batch emulsion polymerization were grafted easily, with 90.2% grafting efficiency of the corresponding core-shell elastomer. The grafting efficiency of the rubber particles prepared by acid agglomeration was only 69.4%. The former was most suitable as the toughening core of transparent Acrylonitrile-butadiene-styrene resin, and the transmittance and haze values of the composite were 90% and 2.4, respectively. Impact and tensile strengths were 185.6 J/m and 39 MPa, respectively. The acid agglomeration method generated submicron rubber particles more quickly, and the transmittance and haze of composite were 90% and 2.9, respectively. However, the impact and tensile strengths were reduced to 170.4 J/m and 31 MPa, respectively.