We invesstagated the relationship between the emission efficiency of InGaN/GaN multiple quantum wells (MQWs) and the V-shape pits (V-pits) forming along the threading dislocation (TD). The thinner InGaN/GaN MQWs on the side walls around V-pits would create higher local energy barriers, which can resist the carriers trapped into the non-radiative recombination centres within TDs. By inserting different InGaN/GaN superlattice (SLS) layers below the MQWs, sizes of V-pits could be properly controlled. It was found that the V-pit size on InGaN MQWs increased with increasing SLS layers, which could decrease energy barriers. On the contrary, the shorter distance between the TD center and V-pit boundary would increase the carrier capturing capability of TDs in smaller V-pits. By properly controlling the V-shape defect formation, the best internal quantum efficiency of about 70%f was found in the MQWs with underlying 15 periods SLS layers.