A package unit and a stacking structure thereof are provided. The package unit includes a substrate, a first patterned circuit layer, a first conductive pillar, a semiconductor element, an insulation layer, a second conductive pillar, a third conductive pillar, a second patterned circuit layer and a conductive bump. The first patterned circuit layer is disposed on a surface of the substrate. The first conductive pillar is deposited through the substrate. The semiconductor element is disposed on the substrate. The insulation layer covers the semiconductor element and the substrate. The second conductive pillar is deposited through the insulation layer. The third conductive pillar is deposited through the insulation layer. The second patterned circuit layer is disposed on the insulation layer. The conductive bump is disposed on the second patterned metal layer.