A light emitting diode package structure having a heat-resistant cover and a method of manufacturing the same include a base, a light emitting diode chip, a plastic shell, and a packaging material. The plastic shell is in the shape of a bowl and has an injection hole thereon. After the light emitting diode chip is installed onto the base, the plastic shell is covered onto the base to fully and air-tightly seal the light emitting diode chip, and the packaging material is injected into the plastic shell through the injection hole until the plastic shell is filled up with the packaging material to form a packaging cover, and finally the plastic shell is removed to complete the LED package structure.