This study examined the interaction of indirubin with bovine serum albumin (BSA) at three temperatures (286, 297, 308 K) at pH 7.40. In the presence of indirubin, the drug-BSA binding mode, binding constant and the protein structure changes in aqueous solution were determined by fluorescence quenching methods including Fourier transform infrared (FT-IR) spectroscopy and UV-Vis spectroscopy. The FT-IR change indicates that indirubin binds to BSA. The change in protein secondary structure accompanying ligand binding has been proved by fluorescence spectra data. The thermodynamic parameters, the enthalpy change (DeltaH), and the entropy change (DeltaS) calculated by the van't Hoff equation possess small negative (-2.744 kJ.mol(-1)) and positive values (112.756 J.mol(-1).K(-1)), respectively, which indicated that hydrophobic interactions play the main role in the binding of indirubin to BSA. Furthermore, the displacement experiment shows that indirubin can bind to the subdomain IIA and the distance between the tryptophan residues in BSA and indirubin bound to site I was estimated to be 2.24 nm according to Föster's equation on the basis of fluorescence energy transfer.