A light emitting diode package structure including a base, a light emitting diode and an encapsulant is provided. The light emitting diode is disposed on a surface of the base and is adapted to generate and emit a light. The encapsulant is disposed on the base and encapsulates the light emitting diode. The encapsulant has a surface parallel to the surface of the base and a plurality of surfaces perpendicular to the surface of the base. The light, after passing through the surface of the encapsulant parallel to the surface of the base, has a first light intensity. The light, after passing through the surfaces of the encapsulant perpendicular to the surface of the base, has a second light intensity. The first light intensity is greater than the second light intensity. In addition, a manufacturing method of a light emitting diode package structure is also provided.