To investigate the synergistic effects of silica and absorbed water on the structure and properties of a silica composite rubber (SCR) of cis-1,4-polyisoprene (PI), differential scanning calorimetry analyses were performed. The results show that the specific heat capacity and glass transition point of PI in SCR depend on the silica fraction. In addition, the properties of diffusion and absorption of water change with the silica fractions. The absorbed water exists as nanometer-sized droplets in the polymer networks and affects the glass transition point of PI. It is concluded that the composited silica and absorbed water in SCR exhibit synergistic effects on the structure and thermal properties of SCR.