A chip structure includes first and second semiconductor chips. The first semiconductor chip includes a first semiconductor substrate, a first interconnection layer located on the first semiconductor substrate, a first protection layer covering the first interconnection layer, a gap fill layer located on the first protection layer, and first conductive vias embedded in the gap fill layer and electrically connected with the first interconnection layer. The second semiconductor chip is embedded within the first semiconductor chip and surrounded by the gap fill layer and the first conductive vias, wherein the second semiconductor chip includes a second semiconductor substrate, a second interconnection layer located on the second semiconductor substrate, a second protection layer located on the second interconnection layer, and second conductive vias embedded in the second protection layer and electrically connected with the second interconnection layer, wherein the second semiconductor substrate is bonded to the first protection layer.