Transparent ZnSe/SiO2 nanocomposites were prepared using a sol–gel technique which was followed by a reductive thermal treatment. The several approaches for avoiding the aggregation of ZnSe nanocrystals (NCs) doped in silica gel-glass were presented and adopted compositely during the preparation process. Transmission electron microscopy (TEM), X-ray diffraction (XRD), UV–Vis optical absorption, and Raman scattering were used to study the microstructural properties of the nanocomposites. All nanocomposites were found to show significant finite size effects as characterized by the broadened XRD peaks, blueshifts of the interband optical absorption edge, and the asymmetric broadening of the Raman scatterings. The structure and properties were correlated and discussed.