Metal ions are widely used to achieve selective hydrophobization of different mineral particles. However, the atomic understanding of the roles of metal ions is insufficient due to the limitation of experimental techniques. Herein, the in-situ atomic force microscopy (AFM) force curves and first-principles calculations were combined with the conventional experiments [i.e., batch flotation, zeta potential tests, and X-ray photoelectron spectroscopy (XPS)] to investigate the roles of lead ions (Pb2+) in flotation separation of scheelite and fluorite. The conventional experiments showed that Pb2+ could enhance the flotation recovery of scheelite but suppress fluorite. AFM force curves showed that, due to the presence of Pb2+, the interaction force between benzohydroxamic acid (BHA) and the scheelite surface was a stronger adhesion than the adhesion between BHA and fluorite without lead ions. First-principles calculations revealed that the strong electrostatic attraction resulted in the adsorption of BHA on fluorite surfaces. However, BHA could hardly bond with the scheelite surface with negative charges and hydroxylated Ca sites. The reaction between BHA and Pb2+ was the most favorable. The formed BHA-Pb complexes demonstrated repulsive interactions on fluorite surfaces but attractions on scheelite surfaces. Lead ions played as an inhibitor for fluorite flotation and an on-off switch for scheelite flotation. AFM and first-principles calculations have shown great potential in the analysis of the complicated interface interactions.