The effect of post-growth annealing (PGA) on dot-in-well (DWELL) structures grown on Si substrates has been studied. The photoluminescence (PL) measurements showed that, compared to the DWELL structures directly grown on GaAs, the PGA process induces a distinct difference in the tuning of the emission properties. Then, transmission electron microscopy imaging of the samples revealed that PGA improved the uniformity of quantum dots (QDs) while the size of the QDs increased, in agreement with a corresponding red shift and a decrease of the full width at half maximum in the PL emission spectrum. Finally, energy-dispersive x-ray linescan provided a quantitative analysis of the composition change of DWELL grown on Si in the as-grown, 700°C annealed, and 800°C annealed samples. The change in the In L /Ga K concentration ratio became gradual between the QDs and surrounding materials after 800°C annealing. The analysis of the optical properties, morphology evolution, and compositional change of the QDs as a function of the annealing temperature showed good agreement.