The mismatch of refractive index (RI) between light emitting diode (LED) chips and packaging resins severely lowers the lighting emitting efficacy of LED. The RI can be enhanced by the introduction of high RI nanoparticles but meanwhile it is a great challenge to maintain the high transparency for resins due to the agglomeration of nanoparticles. In this work, a facile strategy is proposed to fabricate silicone nanocomposites with a high transparency (>88%, less than 2% decrease relative to pure silicone resin), largely enhanced RI (an increase from 1.42 to 1.60) and improved thermal stability (73 °C increase in weight loss of 50%). Specifically, the ultra-fine monodispersed TiO2/silicone composites are prepared by direct solvent mixing of 1 wt% surface modified TiO2 nanoparticles (S-TiO2) into the silicone resin, in which S-TiO2 are prepared by direct introduction of titanate coupling agent in the process of TiO2 growth to induce the formation of protective layer on the surfaces of TiO2 nanoparticles. This methodology demonstrated is simple, cost-effective and versatile for the massive fabrication of highly transparent LED packaging materials with greatly enhanced refractive index and meanwhile enhanced thermal stability.