Patterned sapphire substrates (PSS) are fabricated without lithography. Because the patterned sapphire substrate forms naturally, we name it as NPSS. The GaN LED epi-layers are grown by using MOCVD. We analyze the dislocation density and the residual stress of the GaN epi-layer. After the horizontal LED chip process, we find out that the output power of NPSS LED is close to the LED chip chip on the regular patterned sapphire substrate (RPSS). As for white light LED, we find out that LEDs with 5 μm and 4 μm substrate have higher package efficiency than the LEDs on 2 μm and RPSS. Because the light extraction efficiency (LEE) and phosphor absorption affect the white light LED package optical efficiency. To investigate this mechanism, we design experiment to decouple these factors.