The invention provides a three-dimensional fabric filled with aerogel and a preparation method thereof. The three-dimensional fabric filled with aerogel includes a three-dimensional fabric which has two surface yarn layers connected to each other; the aerogel is packed between the two surface yarn layers. The surface yarn layers, as a framework, are combined with the aerogel, so that the product has great mechanical performance, heat-insulation performance and anti-explosion and damping properties. The product has extensive application value in the fields of industry, military industry, aerospace and the like.