A graft copolymer, a thermoplastic resin composition including the graft copolymer, and a method of preparing the thermoplastic resin composition are described herein. A graft copolymer having a shell in which silica modified with a specific compound is dispersed within a specific content range, a thermoplastic resin composition including the graft copolymer, and a method of preparing the thermoplastic resin composition are also described herein. Since silica modified with a specific compound is dispersed in the periphery of rubber particles, that is, in the shell of the graft copolymer, the dispersibility of the graft copolymer may be improved. Therefore, the graft copolymer may have transparency equal to or better than a conventional graft copolymer. In addition, compared to a resin composition having an equivalent rubber content, the thermoplastic resin composition described herein may have excellent physical properties, such as impact strength and tensile strength.