The invention discloses a method for manufacturing a heat dissipation structure for PoP encapsulation. The method for manufacturing the heat dissipation structure for PoP encapsulation comprises the steps that an upper encapsulation substrate is manufactured, wherein thermal vias and a plurality of layers of cooper foil with a large area are arranged in the upper encapsulation substrate, and semi-through holes filled with copper are formed in the periphery of the upper encapsulation substrate; a plurality of upper encapsulation heat conducting chips or devices are attached to or welded to the thermal vias in the upper encapsulation substrate, so that an upper encapsulation body is formed; a lower encapsulation body is manufactured; a bonding pad on the back face of the upper encapsulation substrate is brushed with solder paste, BGA balls are implanted into a steel net, backflow is conducted, and therefore BGA supporting balls are formed; a bonding pad on the upper surface of a lower encapsulation body substrate is brushed with solder paste, after the lower encapsulation bonding pad is flush with the BGA supporting balls of the upper encapsulation body, backflow is conducted, and therefore the upper encapsulation body and the lower encapsulation body are connected with each other; a bonding pad on the back face of the lower encapsulation body substrate is brushed with solder paste, BGA balls are implanted into a steel net, backflow is conducted, and therefore ball implantation on the lower encapsulation body is achieved; a heat dissipation cover is arranged on the top of the upper encapsulation body, and the portion between the upper encapsulation heat conducting chips or devices and the heat dissipation cover is coated with a layer of high-heat-conductivity thermal interface material.