Nanotwin structures are observed in high-resolution transmission electron microscopy studies of cubic phase CdS quantum dots in powder form by chemical co-precipitation method. The deposition of thin films of nanocrystalline CdS is carried out on silicon, glass, and TEM grids keeping the substrates at room temperature (RT) and 200°C by pulsed laser ablation. These films are then subjected to thermal annealing at different temperatures. Glancing angle X-ray diffraction results confirm structural phase transitions after thermal annealing of films deposited at RT and 200°C. The variation of average particle size and ratio of intensities in Raman peaks I2LO/I1LO with annealing temperature are studied. It is found that electron-phonon interaction is a function of temperature and particle size and is independent of the structure. Besides Raman modes LO, 2LO and 3LO of CdS at approximately 302, 603, and 903 cm−1 respectively, two extra Raman modes at approximately 390 and 690 cm−1 are studied for the first time. The green and orange emissions observed in photoluminescence are correlated with phase transition.