The compound 3,3′-diindolylmethane (DIM) has a broad spectrum of anticancer activities. However, low stability and bioavailability limit its application. Elucidating interactions between DIM and β-lactoglobulin (β-LG) may be useful for fabricating whey protein-based protecting systems. Interaction with DIM increased the diameter and absolute zeta potential value of β-LG. UV-absorption spectra suggested that there was a complex of DIM and β-LG. β-LG showed enhanced fluorescence intensity by complexing with DIM with a binding constant of 6.7 × 105 M−1. Upon interaction with DIM, β-LG was decreased in secondary structure content of helix and turn while increased in β-sheet and unordered. FT-IR spectra and molecular docking results indicated the roles of hydrophobic interaction and hydrogen bond for the formation of DIM and β-LG nanocomplexes. Data suggested that β-LG may be a good vehicle for making a protein-based DIM protection and delivery system due to the tight binding of DIM to β-LG.