Circular dichroism (CD) spectra of complexes based on ZnS:Mn/ZnS and CdSe/ZnS quantum dots (QDs) and chlorin e6 (Ce6) molecules in dimethyl sulfoxide (DMSO) and in aqueous solutions at different pH levels were investigated. The changes in CD spectra of Ce6 upon its bonding in complex with semiconductor QDs were analyzed. CD spectroscopy allowed us to obtain the CD spectrum of a luminescent Ce6 dimer and to identify a nonluminescent Ce6 aggregate, which is thought to be a tetramer. The dissymmetry factor of the tetramer is 40 times larger than that of the Ce6 monomer. The analysis of the obtained data showed that in complexes with QDs Ce6 can be either in the monomer form or in the form of a nonluminescent tetramer. The interaction of the relatively unstable luminescent Ce6 dimer with QDs leads to its partial monomerization and the formation of complexes with Ce6 in the monomer form. On the basis of time-dependent density functional theory calculations, we performed a geometry model of Ce6 dimer form with corresponding calculated absorption and CD spectra, which are in a qualitative agreement with the experimental data.