We used low-temperature reactions to synthesize different-sized CdSe quantum dots (QDs) capped with fatty-acid and phosphine ligands. From the correlation of high-resolution transmission electron microscopy and X-ray diffraction (XRD) analyses of the synthesized QDs, we observed size-dependent shape anisotropy. In addition, the recorded XRD patterns revealed mixed crystal facets with zinc blende and wurtzite structures in small-sized QDs. Furthermore, from differential absorption (DA) spectra, we extracted the electronic transition energies for different-sized QDs, which were found to be similar to the calculated values of the quantum size levels associated with band mixing of CdSe QDs with a moderate bandgap. We found that the excitonic absorption peaks are increasingly "hidden" with decreasing QD size because of the crystal structure and crystalline quality. The results show good agreement with the obtained diffraction patterns and the estimation errors obtained from the DA spectra.