The invention discloses an organic silicon pouring sealant and a preparation method thereof. The organic silicon pouring sealant comprises a component A and a component B with the same mass, wherein the component A comprises a base material, dual vinyl-terminated silicone oil, methyl silicone oil and a platinum catalyst; the component B comprises the base material, the methyl silicone oil, hydrogen-containing silicone oil, a hydrogen-terminated silicone oil, a tackifier, black slurry and an inhibitor; the base material comprises the dual vinyl-terminated silicone oil, a heat-conducting fillerand a filler treating agent; the tackifier is a silane coupling agent with epoxy groups and vinyl groups; and the filler treating agent is silane with 12-20 carbons. The preparation method of the organic silicon pouring sealant comprises the following steps of preparing the base material, the component A and the component B; and finally, uniformly mixing the prepared component A and the prepared component B, and carrying out vacuumizing to remove bubbles, thereby obtaining the organic silicon pouring sealant. The organic silicon pouring sealant has the excellent flow performance, the high viscosity and the low stress, and the stress can reach shore OOO 1 or below.