The invention belongs to the field of electronic polymer materials and discloses an organic silicon electronic-pouring sealant with high refractive index and high transparency, as well as a preparation method and an application thereof. The method comprises the following steps of: adding olefin-based silane and a silanol type compound into an organic solvent, adding a catalyst, and reacting at the temperature of 50-100 DEG C for 3-12h to get an olefin-based silane oligomer precursor; dripping an olefin-based silane coupling agent solution into a mercapto-compound solution, and reacting at the temperature of 50-100 DEG C for 8-48h to get a mercaptosilane oligomer precursor; mixing the two precursors to get the organic silicon electronic-pouring sealant, and the curing method comprises the following steps of heating to the temperature of 80-140 DEG C and curing for 3-8h, wherein the refractive index after curing is 1.53-1.59, and the light transmittance is 94-99%. According to the preparation method disclosed by the invention, phenyl and a sulfur element are introduced into the organic silicon electronic-pouring sealant, a thermocuring cross-linking technology is adopted, and mercapto-alkenyl click chemistry thermocuring can occur rapidly, so that the refractive index, the light transmittance and the mechanical properties after curing can be improved.