Nobiletin (Nob) is a major component among the most reported polymethoxyflavones (PMFs), which possesses multiple efficacious healthcare activities. Owing to its high melting point and poor water solubility, the oral bioavailability of Nob needs to be improved via loading Nob on carriers. To take full advantage of Nob, the interaction mechanism between Nob and vehicles should be clarified. Herein, β-lactoglobulin (β-LG) was selected as the vehicle and further investigated the binding mechanism between Nob and β-LG. The binding stoichiometry of complex was found to be 1:1 by analysis of intrinsic fluorescence experiment. The results also confirmed by isothermal titration calorimetry (ITC) measurement that the binding behavior between β-LG and Nob was a spontaneously endothermic process driving mainly by hydrophobic interaction. Moreover, competitive binding and molecular docking method indicated the Nob was primary bound to internal calyx of β-LG at neutral pH. UV spectrophotometry revealed that the solubility of Nob was enhanced to 3 times by forming complex. Furthermore, Nob could alter secondary structure of β-LG by a transition from α-helix to β-sheet and lead to small increase on surface hydrophobicity of β-LG. This work will provide some valuable information on clarifying the interaction between protein and PMFs, which contributing to improve the poor bioavailability of PMFs.