The network and the hairy structures expected to be formed on the filler surface by the treatment with trialkoxy and dialkoxy types of silane coupling agent (SCA) having mercapto group, respectively. The stress-strain curve of the filled isoprene rubber (IR) composite was investigated. The 300% modulus was higher in the dialkoxy than in the trialkoxy system. The entanglement of SCA and IR chains tends to occur in the dialkoxy system. The loose network structure is formed by the mixture of dialkoxy and smaller amount of trialkoxy types. The loose network was more effective to improve the 300% modulus. The interpenetrating polymer networks (IPN) by the SCA and IR chains expected to be formed at the interface. In order to reinforce the IR composite with calcium carbonate particles, the surface treatment with a mixture of amino- and mercapto-functional SCAs was useful. Interaction between the amino group and the calcium carbonate surface, covalent bonding between the mercapto group and the IR, and dense network formation of trialkoxy SCAs were important for improving the mechanical properties.