Quantum dots in nanowires (DINWs) are considered as important building blocks for novel nanoscale semiconductor optoelectronic devices. In this paper, pure axial heterojunction InGaN/GaN DINWs are grown by using plasma-assisted molecular beam epitaxy (PA-MBE) system. The InGaN quantum dots (QDs) are disk-like observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The diameter of QDs can be controlled by the growth conditions of nanowires (NWs), while the thickness of QDs can be controlled by the growth time of InGaN. Temperature-dependent photoluminescence (TDPL) measurements demonstrate that the PL peak of DINWs with small and uniform sizes shows a general red shift with increasing temperature. However, the PL peak of DINWs with non-uniform sizes shows an abnormal blue shift with increasing temperature, which is due to different internal quantum efficiencies of the DINWs with different sizes.