The influences of alkoxy group number and loading method of silane coupling agents on the mechanical properties of a styrene-butadiene rubber/silica composite were investigated. Mercapto functional silane coupling agents with dialkoxy and trialkoxy structures were used. The pre-treatment method and the integral blend method were compared. Both the fracture stress and modulus at 200% strain were higher in the pre-treatment than in the integral blend for dialkoxy type composites. However, they were higher in the integral blend than in the pre-treatment for trialkoxy-type composites. The interaction between the silane chains on the silica surface and the rubber molecular chains at the interfacial region was estimated by H-1 pulse nuclear magnetic resonance spectroscopy using an unvulcanized silica/rubber mixture. It was found that the binding of rubber molecular chains by the silane chains was higher in the pre-treatment system for dialkoxy-type composites, whereas it was higher in the integral blend for trialkoxy-type composites. The reason is proposed as follows: in the pre-treatment for dialkoxy type, a linear silane chain formed in the case of multi-layer coverage. The silane chain entangled with the rubber chain in the interfacial region and improved the reinforcement effect. For the trialkoxy type, a network structure formed using the pre-treatment method, lowering the amount of entanglement. However, in the integral blend for trialkoxy type, the formation of the silane network and the entanglement progressed simultaneously during the preparation process. A well-entangled interfacial region was formed.