A method of making a white LED package structure having a silicon substrate comprises providing a silicon substrate and performing an etching process to form a plurality of cup-structures on a top surface of the silicon substrate. Next, a reflective layer on the top surface of the silicon substrate is formed, and a transparent insulating layer on the reflective layer is formed. Subsequently, a plurality of blue LEDs are respectively bonded in each cup-structure, wherein the blue LEDs have various wavelengths. Last, a plurality of kinds of phosphor powders corresponding to the wavelengths of the blue LEDs are mixed with each other and added to a sealing material, and a sealing process is performed to form a phosphor structure on the cup-structures.