Nowadays, the study of preparing silica/rubber composites, which can be used in “green tire”, in energy saving method is fast-growing. In our work, silica modified by using alcohol polyoxyethylene ether (AEO) and 3-Mercaptopropyltriethoxysilane (K-MEPTS) together were investigated. Thermal gravimetric analyzer (TGA) result indicated that both AEO and K-MEPTS could be grafted on the silica surface. Raman spectroscopy confirmed that the AEO could generate a certain steric hindrance for the mercaptopropyl group on K-MEPTS. Silica modified by using AEO and K-MEPTS together can be completely co-coagulated with the rubber in preparing silica/natural rubber (NR) composites by latex compounding method. AEO can form a physical interface between silica and rubber; meanwhile, K-MEPTS can form a chemical interface between silica and rubber. The effects of chemical and physical interface between silica and rubber on dynamic and mechanical performances of silica/NR composites were also given in this research. A proper combination of physical and chemical interface between silica and NR can improve performances of silica/NR composites.