We investigated the effect of rapid thermal annealing from 700 °C to 950 °C on stacked InAs/GaAs quantum dots (QDs) covered with GaAs and In0.19Ga0.81As layers. Large blue-shift of the energy positions nearly 380 meV (1187 nm to 870 nm) have been observed in InGaAs capped samples together with improvement in the photoluminescence integrated intensity of more than five times. The strong narrowing of the photoluminescence line-width in both GaAs (as narrow as 8 meV) and InGaAs capped samples show an improvement of the size distribution of the QDs. In addition, a significant reduction of the energy spacing (ΔE2-1) between ground state and first excited state emissions were found in both GaAs and InGaAs capped quantum dots due to interface inter-diffusion induced by thermal treatment. The excited state filling experiments for InGaAs capped sample annealed at 950 °C exhibits quantum well like behavior where as, the GaAs capped sample shows a shoulder in high energy side might be due to first excited state of QDs.