A multi-chip stacking structure and a manufacturing method thereof are disclosed, comprising the steps of: providing a lead shelf including a chip seat and a plurality of feet to respectively dispose a first and a second chips on two surfaces of the chip seat; disposing the lead shelf on a heating block provided with a concave hole at the time of welding wire, such that the lead shelf is supported on the heating block and the second chip is contained in the concave hole, then carrying out the first wire bonding operation so that the first chip is electrically connected with the foot via a first welding wire, in the meantime, equipping a protruding block at one side of the foot which is correspondingly connected with the first welding wire, then reversely disposing the lead shelf to be supported on the heating block via the protruding block, and containing the first chip and the first welding wire in the concave hole of the heating block, afterwards, carrying out the second wire bonding operation so that the second chip is electrically connected with the foot via a second welding wire. Accordingly, the feet are supported by certain height through the protruding block, which avoids the heating block from contacting the welding wires, and the heating block is in no need of replacement.