II–VI semiconductor nanoparticle systems can be prepared by keV high-dose ion implantation and subsequent thermal annealing. The ternay Cd–S–Se system offers an additional degree of freedom to adjust materials properties, as Se and S are completely miscible on the Se sublattice. X-ray diffraction analysis indicates, that hexagonal CdS x Se 1−x nanocrystals are formed after rapid thermal annealing. Peak positions are evaluated using Vegard’s law. Material loss is monitored quantitatively by Rutherford backscattering spectroscopy (RBS). Cross-sectional TEM images are revealing strong influence of the composition on the nanocrystal structural evolution.