A three-dimension circuit structure includes a substrate, a first conductive layer, a filled material and a second conductive layer. The substrate has an upper surface and a cavity located at the upper surface. The first conductive layer covers the inside walls of the cavity and protrudes out the upper surface. The filled material fills the cavity and covers the first conductive layer. The second conductive layer covers the filled material and a portion of the first conductive layer, and the first conductive layer and the second conductive layer encapsulate the filled material. The material of the filled material is different from that of the first conductive layer and the second conductive layer.