The effects of thermal annealing treatment on a vertically aligned InGaAs/GaAs(Sb)/AlGaAsSb quantum dot (QD) structure with the purpose of tailoring energy band alignment are studied. In contrast to the typical blue-shift in the emission upon annealing because of In−Ga intermixing in the typical InGaAs/GaAs QDs, thermally annealed InGaAs/ GaAs(Sb)/AlGaAsSb QDs exhibit a red-shift upon annealing at 700 °C, owing to Sb aggregation on top of the InGaAs QDs, resulting in tailoring of the band alignment and strain reduction for the reduced emission energy. Power-dependent and time-resolved photoluminescence were utilized herein to extend the carrier lifetime from 1.63 ns to 6.38 ns and to elucidate mechanisms of the aggregation of antimony that cause the energy band alignment modifying from type I to type II after rapid thermal annealing. In addition, the thermal stability of the columnar QDs was improved by capping QDs with a GaAsSb overgrown layer, because In−Ga intermixing was suppressed, helping to preserve the QD heterostructures. Therefore, the flexible modulation of energy band alignment for columnar InGaAs/GaAs(Sb)/AlGaAsSb QD structures as type I or type II by thermal annealing has potential and flexible applications to versatile QD-related optoelectronic devices.