The binding of BDE47 to lysozyme was investigated by molecular modeling combined with three-dimensional (3D) fluorescence, circular dichroism (CD) techniques, fluorescence spectroscopy, and time-resolved fluorescence decay under simulative physiological conditions. The results indicated that the quenching reaction of BDE47 to lysozyme was observed, and the quenching mechanism was suggested as static quenching. Molecular docking showed that the amino acid residues, TRP62, TRP63, ARG61, ASN59, ALA107, ILE98 in lysozyme have interactions with BDE47. The hydrogen bonds were formed between the O atom of BDE47 and TRP62 with the distances of 2.2 . The 3D fluorescence experiments showed that the fluorescence intensity of lysozyme gradually decreased in the presence of BDE47 and a red shifted was observed, suggesting that the microenvironment around the TRP-residues of lysozyme has changed during the binding process. Furthermore, CD spectra implied that the interaction of BDE47 with lysozyme induced conformational change of lysozyme, and the content of α-helix structures in lysozyme decreased. The binding distance r between the donor (lysozyme) and acceptor (BDE47) calculated using Frster’s nonradiative energy transfer theory was 3.31 nm, indicating a high probability of energy transfer from lysozyme to BDE47. The thermodynamic parameters at different temperatures indicated that the hydrogen bonds and van der Waals forces played a predominant role in the spontaneous binding process. The results were consistent with the molecular docking and binding free energy analysis.