A strategically constructed substrate, patterned sapphire with silica array (PSSA), was developed to boost the efficiency of patterned sapphire substrate (PSS) in GaN-based light-emitting diodes (LEDs) application. The light output power of a flip-chip LED on PSSA improved by 16.5% at 120 mA than that of device grown on PSS. The XRD and STEM measurements revealed that the GaN epilayer grown on PSSA had better crystalline quality compared to the epilayer grown on PSS, which was the result of decreased misfit at coalescence boundary in the PSSA case. Moreover, the light extraction efficiency of the flip-chip LED on PSSA was significantly enhanced, benefiting from the small refractive-index contrast between the patterned silica array and air. This small refractive-index contrast also contributed to a more convergent emission pattern for the flip-chip LED on PSSA, as demonstrated by the far-field radiation pattern measurements. The discovery that PSSA could excel at defect suppression and light extraction revealed a new substrate platform for III-nitride optoelectronic devices.