A light-emitting diode (LED) package structure includes a substrate, an LED, a side wall, an encapsulant, and a waterproof protective coating. The LED is disposed on the substrate, the side wall defines a through hole and is disposed on the substrate, and the LED is accommodated in the through hole. The encapsulant is filled in the through hole and covers the LED. A heterojunction is disposed between the encapsulant and the side wall, and the waterproof protective coating seals the heterojunction. Furthermore, the encapsulant includes a first fluoropolymer, the waterproof protective coating includes a second fluoropolymer, and the light transmittance of the first fluoropolymer is greater than that of the second fluoropolymer.