A light-emitting diode chip structure including a conductive substrate, a semiconductor stacking layer and a patterned seed crystal layer is provided. The conductive substrate has a surface. The surface has a first region and a second region alternately distributed over the surface. The semiconductor stacking layer is disposed on the conductive substrate, and the surface of the conductive substrate faces the semiconductor stacking layer. The patterned seed crystal layer is disposed on the first region of the surface of the conductive substrate and between the conductive substrate and the semiconductor stacking layer. The patterned seed crystal layer separates the semiconductor stacking layer from the first region. The semiconductor stacking layer covers the patterned seed crystal layer and the second region, and is electrically connected to the conductive substrate through the second region. A fabrication method of the light-emitting diode chip structure is also provided.