Objective To investigate the effects of different NaCl concentrations on the binding of proteins to small molecules.Methods The β-lactoglobulin and anthocyanin were selected as the target protein and small molecule, respectively. Molecular dynamics simulations were conducted to study the binding patterns and protein structural changes under five NaCl concentrations (0, 0.25, 0.50, 0.75, and 1.00 mol/L).Results Anthocyanin mainly bound to the hydrophobic cavity of β-lactoglobulin. In the 150 ns molecular dynamics simulations, the protein structure remained stable at each NaCl concentration, and its binding with the small molecule was steady. However, with the increase in NaCl concentration, the hydrogen bonds between proteins, hydrophobic surface area, and α-helix content decreased, while the β-sheet content increased within the 0.75 mol/L NaCl concentration range. The binding free energy of the two components first increased with NaCl concentration, reached a maximum at 0.50 mol/L, and then gradually decreased. At 1.00 mol/L, it was even much lower than the control group, mainly due to the simultaneous weakening of van der Waals forces, hydrogen bonding, and hydrophobic interactions under 1.00 mol/L NaCl. Small molecules also moved from the interior of the hydrophobic cavity toward the surface at the protein binding site.Conclusion The amount of NaCl added in the food system significantly affects the binding of proteins to small plant molecules, which may further affect the properties of proteins and the biological activity of small molecules.