The strucrture of CdS quantum dots 0,3% (mass), stabilized by the solution of the mercaptosuccinic acid in the gel matrix 50% THEOS is investigated by small-angle X-ray scattering (SAXS). Application of modern methods of SAXS data interpretation, including procedure of ab initio modeling of particle structure, allowed us for the to reveal structural organization of both individual nanoparticles and of their clusters incorporated in the polymer matrix. As a result, the shape, size, and size distribution of the obtained nanoparticles and their clusters depended on the structure of the gel matrix used as a formation medium.