Silica particles were treated by silane coupling agents to study the effects of surface chemistry of silica particles on the secondary structure formed by silica particles in styrene-butadiene rubber (SBR). The relation between the size of secondary structure and tensile properties of silica-filled SBR vulcanizates was also investigated. The water molecules adsorbed on the silica surface enhanced both the reactivity of the coupling agents with silanol groups on the silica surface and the condensation reaction between coupling agents. The averaged size of one agglomerate in the filled vulcanizate ((Sagg) over bar) decreased with the increase of the hydrophobic character of silica particles, which were obtained by the introduction of coupling agents with alkyl groups. The initial slope of stress-strain curves for silica-filled vulcanizates decreased with the decrease of (Sagg) over bar. Further, a clear Payne effect was in all silica-filled vulcanizates, with this tendency more prominent in the larger Sagg.