In this paper, we have observed an atomic-scale structure and compositional variation at the interface of the InGaN/GaN multi-quantum wells (MQW) by both scanning transmission electron microscopy (STEM) using high-angle annular dark-field mode and atom probe tomography (APT). The iso-concentration analysis of APT results revealed that the roughness of InGaN/GaN interface increased as the MQW layers were filled up, and that the upper interface of MQW (GaN/InGaN to the p-GaN side) was much rougher than that of the lower interface (InGaN/GaN tot he n-GaN side). On the basis of experimental results, it is suggested that the formation of interface roughness can affect the quantum efficiency of InGaN-based light-emitting diodes.