The microstructural study of InGaN/GaN multiple quantum well (MQW) structures with high In (indium) composition (> 30%) has been performed using transmission electron microscopy (TEM). The increased strain in InGaN/GaN MQWs by high In composition is relaxed by the formation of several defects such as dislocations, stacking faults, V-defects, and tetragonal shape defects. High-resolution TEM (HRTEM) measurement shows a new formation mechanism of V-defects, which is related to the stacking mismatch boundary induced by stacking faults. These V-defects result in different growth rates of the GaN barriers according to the degree of the bending of InGaN well layers, which changes the period thickness of the superlattice. In addition, evidence of In clustering is directly observed both by using an In ratio map of the MQWs and from In composition measurements along an InGaN well using energy filtered TEM (EFTEM).