To improve the interfacial interaction in clay/SBR nanocomposites prepared by latex compounding method, a novel clay modification for the nanocomposites was introduced before latex compounding with SBR using three kinds of organic modifiers, namely, hexadecyl trimethyl ammonium bromide (C16), bis(hexadecyl) dimethyl ammonium bromide (DC16) and 3-aminopropyl triethoxy silane (KH550). On the other hand, bis(triethoxysilylpropyl)tetrasulfide (Si69) was added into the KH550 modified clay/SBR nanocomposite during later mechanical blending, and was designed to interact with both KH550 and rubber and thus improve the interface. Structure changes of the nanocomposites were followed by study of X-ray diffraction, transmission electron microscopy and rubber process analyzer. Dynamic mechanical analysis and tensile tests were carried out to obtain information about the mechanical properties of the nanocomposites. The results revealed that, with the organic modification, clay was dispersed finely in the rubber matrix with part rubber-intercalated or part modifier-intercalated structure. Compared with the unmodified nanocomposite, the tensile strength, the stress at 300% strain, and the tear strength of modified SBR-clay nanocomposites were significantly improved. Moreover, the type of modifiers and strength of interfacial interaction determined the properties of the nanocomposites. The incorporation of KH550 and Si69 brought the best modification effect among all the modification methods.