We performed depth-resolved PL and Raman spectral mappings of a GaN-based LED structure grown on a patterned sapphire substrate (PSS). Our results showed that the Raman mapping in the PSS-GaN heterointerface and the PL mapping in the In x Ga 1-x N/GaN MQWs active layer are spatially correlated. Based on the 3D construction of E 2 (high) Raman peak intensity and frequency shift, V-shaped pits in the MQWs can be traced down to the dislocations originated in the cone tip area of PSS. Detail analysis of the PL peak distribution further revealed that the indium composition in the MQWs is related to the residual strain propagating from the PSS-GaN heterointerface toward the LED surface. Numerical simulation based on the indium composition distribution also led to a radiative recombination rate distribution that shows agreement with the experimental PL intensity distribution in the In x Ga 1-x N/GaN MQWs active layer.