The properties of styrene-butadiene rubber (SBR) reinforced by modified silica was investigated according to national standards. Silica was modified by silane coupling agents KH-570, KH-590, and KH-792. The optimized geometries of molecular modified silica reinforced SBR were obtained by using B3LYP calculation of density functional theory with the 6-31+G basis sets. The natural bond orbital analyses were carried out. The Si-O bond length of silica modified by KH-792 was the shortest and the electronegative of O was the highest. It indicated that the connection between silica and KH-792 was the tightest. Higher tensile strength and elongation of reinforced SBR was obtained by silica modified with the KH-792. It was caused by large delocalization of lone pair electrons of the two N atoms in KH-792. The S-C bond length in silica modified by KH-590 was longer than the ordinary S-C bond length. Then the sulfur free radical (·S·) was produced more easily in vulcanization. The degree of crosslink was increased by the cross-linkage of the rubber molecule and the sulfur free radical. That was why the highest stress and tear strength of reinforced SBR was produced when silane coupling agent KH-590 was used. The calculation results was in accord with experimental data.