The invention discloses a manufacturing method of a high-order multistage HDI (High Density Interconnection) printed circuit board. An expansion coefficient of a cross-band veneer is pre-compensated according to a layer number, a dead hole stacking number and an engineering pre-designed lamination structure of a product, a press frequency and a material characteristic; a reference target coordinate, a shape, a size, a process aligning manner and the like are aligned for design demands for systematizing different graph levels and production positioning reference points, so that the alignment matching index and the expansion alignment precision among different levels and different components can be achieved; all the alignment problems caused by various factors in a production process of a three-stage HDI printing circuit can be considered; the alignment problems among a series of important PCB (Printed Circuit Board) processes, such as an inner layer graph, a secondary outer layer circuit, a secondary outer layer buried hole, an outer layer circuit, a mechanical through hole, a radiation dead hole and solder resistance of a one-stage HDI product, a two-stage HDI product and a three-stage HDI product, can be solved; and meanwhile, the hole overlapping precision of micro dead holes and the alignment precision matching indexes of the dead holes, the through hole and a circuit graph can be ensured.