A package structure including a first circuit board, a second circuit board, an encapsulant, a plurality of conductive terminals, and a package device is provided. The first circuit board has a first top surface and a first bottom surface opposite to each other. The second circuit board has a second top surface and a second bottom surface opposite to each other. The encapsulant encapsulates the first and second circuit boards. The conductive terminals are disposed on the first or second bottom surface and electrically connected to the first or second circuit board. The package device is disposed on the first or second top surface and electrically connected to the first and second circuit boards. The package device includes a first chip, a second chip, a chip encapsulant, a circuit layer, and a plurality of conductive package terminals. A manufacturing method of a package structure is also provided.