A LED (light emitting diode) packaging structure includes a base, a LED chip, a gel-blocking structure and a phosphor layer. The LED chip disposed on the base and electrically connected to the base. The LED chip having a substrate and a semiconductor layer formed on the substrate. The gel-blocking structure is disposed on the substrate of the LED chip and surrounding the semiconductor layer. The phosphor layer is filled within a space defined by the gel-blocking structure, the substrate and the semiconductor layer. The present invention also discloses a fabricating method of the LED packaging structure.