The understanding of the correlation between structural and photoluminescence (PL) properties of self-assembled semiconductor quantum dots (QDs), particularly InGaAs QDs grown on (001) GaAs substrates, is crucial for both fundamental research and optoelectronic device applications. So far structural and PL properties have been probed from two different epitaxial layers, namely top-capped and buried layers respectively. Here, we report for the first time both structural and PL measurements from an uncapped layer of InGaAs QDs to correlate directly composition, strain and shape of QDs with the optical properties. Synchrotron X-ray scattering measurements show migration of In atom from the apex of QDs giving systematic reduction of height and enlargement of QDs base in the capping process. The optical transitions show systematic reduction in the energy of ground state and the first excited state transition lines with increase in capping but the energy of the second excited state line remain unchanged. We also found that the excitons are confined at the base region of these elliptically shaped QDs showing an interesting volume-dependent confinement energy scaling of 0.3 instead of 0.67 expected for spherical dots. The presented method will help us tuning the growth of QDs to achieve desired optical properties.