The binding of quercetin to lysozyme (LYSO) in aqueous solution was investigated by fluorescence spectroscopy, UV-vis absorption spectroscopy and molecular simulation at pH 7.4. The fluorescence quenching of LYSO by addition of quercetin is due to static quenching, the binding constants, K ( a ), were 3.63 × 10(4), 3.31 × 10(4) and 2.85 × 10(4) L·mol(-1) at 288, 298 and 308 K, respectively. The thermodynamic parameters, enthalpy change, ∆H, and entropy change, ∆S, were noted to be -7.56 kJ·mol(-1) and 61.07 J·mol(-1)·K(-1). The results indicated that hydrophobic interaction may play a major role in the binding process. The distance r between the donor (LYSO) and acceptor (quercetin) was determined as 3.34 nm by the fluorescence resonance energy transfer. The synchronous fluorescence spectroscopy showed the polarity around the tryptophan residues increased and the hydrophobicity decreased. Furthermore, the study of molecular simulation indicated that quercetin could bind to the active site (a pocket made up of 24 amino-acid residues) of LYSO mainly via hydrophobic interactions and that there were hydrogen interactions between the residues (Gln 57, Ile 98) of LYSO and quercetin. The accessible surface area (ASA) calculation verified the important roles of tryptophan (Trp) residues during the binding process.