Silica is reinforcing filler with high polarity, leading to the difficulty to get the homogenous mixing with a natural rubber (NR) compound, which normally becomes silica agglomeration. A silane coupling agent is applied in a silica-filled NR compound in order to enhance compatibility between silica and rubber. Moreover, non-rubber components, especially proteins, are believed to have competition with silane coupling agent during a silanization [1, 2]. In this work, the interaction between the silane coupling agent and silica-filled NR materials was investigated to show the components influencing in the filler-filler and filler-rubber interaction as well as mechanical properties. The rubber types with different non-rubber components such as fresh NR, deproteinized NR (DPNR) and polyisoprene rubber (IR), absence of non-rubber constituents were mixed with bis-triethoxysilylpropyl disulfide (TESPD) and silica by using an internal mixer at high temperature. Payne effect of the unvulcanised rubber samples were characterized to study silica dispersion, respectively. A swelling test was used to determined crosslink density in the rubber samples after a vulcanisation system. In addition, the effect of non-rubber components on mechanical properties of rubbers was investigated to find the relationship between the crosslink density and filler-rubber network.