In this study we present modifications in a phonon confinement model in order to obtain a better description for the Raman spectra of spherical nanocrystals, namely: bare-core, core–shell, and core–multishell. Our new interpretations allow investigating the influences of the interfacial alloying and strain effects on the vibrational spectra of core–shell nanocrystals. The robustness of the modified phonon confinement model was confirmed by precisely describing the Raman spectra of wurtzite CdSe/CdS core–shell magic-sized quantum dots (CS-MSQDs) synthesized directly in aqueous solution by a new route. The CdSe MSQD sample was used as template to growth CdSe/CdS CS-MSQDs with different shell thickness by setting the synthesis temperature. By using our modified model to fit the Raman spectra of samples, we have obtained the size dimensions of CS-MSQDs (core-diameter and shell-thickness), in excellent agreement with the values obtained by the atomic force microscopy results, confirming that the change in the synthesis temperature is a simple and efficient way to control the CdS-shell thickness during the growth process. Furthermore, we have confirmed the formation of an alloy layer (CdS_xSe_1-x) at the interface of these CdSe/CdS CS-MSQDs and that the strain effects can be neglected for the wurtzite structure.