Spectral properties of hydrophilic associates of colloidal CdS quantum dots (QDs) with methylene blue molecules (MB) prepared by sol–gel method have been studied. The two basic types of hybrid associates were found using FTIR spectra technique. The first-type associates are characterized by planar location of MB heterocycle on QDs spherical interface. In this case MB dimerization is not observed. Both nitrogen and sulfur heteroatoms and double =N+–(CH3)2 bonds of MB are participants of association which causes to conformation of MB heterocycle and π-conjugation length decrease. In UV–Vis absorption and luminescence spectra blue shift of MB peaks for QD-MB associates in comparison with MB spectra in solutions and gelatin was found. The second type of association mostly involves MB nitrogen heteroatoms and CdS QDs interface atoms. At the same time, peaks of UV–Vis and luminescence spectra are red shifted. In this case, dimerization manifestation of MB in QD-MB associates was found. Using the time correlated single photon counting technique resonance electronic excitation energy transfer from recombination luminescence center of CdS QDs to MB molecules was found. Its efficiency is in the range of 0.36–0.51.