A manufacturing method of an LED package structure includes the steps as follows: providing an LED package structure assembly, which has a substrate layer, an LED chip set located on the substrate layer, and an encapsulating gel layer covering the LED chip set; taking a first blade to saw the LED package structure assembly from the encapsulating gel layer to the substrate layer until a plurality of sawing grooves are formed on the substrate layer; and taking a second blade to saw the LED package structure assembly along each sawing groove until the second blade passes through the substrate layer, thereby forming a plurality of LED package structures separated from each other. Wherein a hardness of the first blade is greater than that of the second blade, and a thickness of the second blade is less than that of the first blade.