A three-dimensional stacking structure and the manufacturing method(s) thereof are described. The stacking structure includes at least a bottom die, a top die and a spacer protective structure. The bottom die include contact pads in the non-bonding region. The top die is stacked on the bottom die without covering the contact pads of the bottom die and the bottom die is bonded with the top die through bonding structures there-between. The spacer protective structure is disposed on the bottom die and covers the top die to protect the top die. By forming an anti-bonding layer before stacking the top dies to the bottom dies, the top die can be partially removed to expose the contact pads of the bottom die for further connection.