The chlorophyll fluorescence, photochemical activity and surface electric properties of thylakoid membranes with different stoichiometry of pigment-protein complexes and organization of the light-harvesting chlorophyll a/b protein complex of photosystem II (LHCII) were studied in the presence of substituted 1,4-anthraquinones. Data show strong dependence of the quenching of the chlorophyll fluorescence on the structural organization of LHCII. The increase of the LHCII oligomerization, which is associated with significant reduction of the transmembrane electric charge asymmetry and electric polarizability of the membrane, correlates with enhanced quenching effect of substituted 1,4-athraquinones. Crucial for the large quinone-induced changes in the membrane electric dipole moments is the structure of the quinone molecule. The strongest reduction in the values of the dipole moments is observed after interaction of thylakoids with 3-chloro-9-hydroxy-1,4-anthraquinone (TF33) which has the highest quenching efficiency. The quinone induced changes in the photochemical activity of photosystem II (PSII) correlate with the total amount of the supramolecular LHCII-PSII complex and depend on the number of substituents in the 1,4-anthraquinone molecule.