We report the effect of the capping layer on the optical and structural properties in InGaN/GaN multiple quantum wells of high indium content by using photoluminescence and transmission electron microscopy. For the MQW structure of high indium content, V-defects are mainly formed at the inversion domain boundaries (IDBs) with a translation vector of R = c/2 within the highly strained InGaN/GaN MQWs. We found that using an Al0.1Ga0.9N capping layer with a tensile strain resulted in a transition of the dominant emission from a quantum-dot-like structure (3-d) to a quantum well (2-d) and in an increase in the defect density. The origin of the transition of the dominant emission peak is the disappearance of quantum dot-like structures at the apex of the V-defect due to Al incorporation through the lDBs during the growth of the Al0.1Ga0.9N capping layer.