A manufacturing method of the light-emitting diode package structure is provided. A carrier is formed. The carrier comprises a first build-up circuit. At least one self-assembled material layer is formed on the first build-up circuit. A first solder mask layer is formed on the first build-up circuit. The first solder mask layer has at least one opening to expose a portion of the at least one self-assembled material layer. At least one light-emitting diode is disposed on the first build-up circuit. The at least one light-emitting diode has a self-assembled pattern, and the at least one light-emitting diode is self-assembled into the at least one opening of the first solder mask layer through a force between the self-assembled pattern and the at least one self-assembled material layer.