The light-harvesting complex, LH1, of thermophile purple bacteria Thermochromatium tepidum consists of an array of α- and β-polypeptides which assemble the photoactive bacteriochlorophyll and closely interact with the membrane-lipids. In this study, we investigated the effect of calcium and manganese ions on the protein structure and thermostability of the reaction centre (RC)–LH1/lipid complex. The binding of Ca2+, but not Mn2+ is shown to shift the LH1 Qy absorption maximum from ~889 to 915 nm and to significantly raise the thermostability of the RC–LH1 complex. The ATR–FTIR spectra indicate that interaction of Ca2+ as monitored by the carboxylates’ vibration of aspartate residues, but not Mn2+ induces changes in the α-helix packing arrangement. The reduced rate of 1H/2H exchange of proteins’ amide protons shows that the accessibility to 2H2O is significantly lowered in Ca2+-substituted RC–LH1/lipid complexes. In particular, exchange with the associated lipid molecules, is significantly retarded. These results suggest that the thermostability of the RC–LH1 complex is raised by the distinct interaction with calcium cations which reduces the RC–LH1/lipid dynamics, particularly, at the membrane–water interface.