Sodium-diisobutyl dithiophosphinate (3418A) is a new collector with good selectivity for lead and copper ore, even better than dibutyl dithiophosphate (DTP). However, there still exists a lack of research on a mechanism for the interaction between chalcopyrite and 3418A. In this study, micflotation, microcalorimetric, cyclic voltammetry, adsorption measurement, density functional theory (DFT) calculations, and molecular dynamics (MD) were carried out to investigate the adsorption behaviors and differences of DTP and 3418A on the chalcopyrite surface. The flotation results show that 3418A has higher chalcopyrite recoveries than DTP, and microcalorimetric and adsorption measurements indicate that the adsorption quantity and adsorption heat of 3418A on the chalcopyrite surface is higher than that of DTP. In addition, DFT calculations suggest that the chemical adsorption of 3418A on the chalcopyrite surface is stronger than that of DTP. MD simulation results suggest that the hydrophobicity of the chalcopyrite surface after 3418A adsorption is stronger than that of DTP. Hence, our results presented that the 3418A is more favorable to the flotation of chalcopyrite than DTP. Based on coordination chemistry theory, the orbital interaction between chalcopyrite and reagent molecules is analyzed. It is suggested that the interaction between DTP and chalcopyrite is positive σ action, as well as 3418A, while the π back-bonding has not occurred. In addition, the energy of the highest occupied molecular orbital (HOMO) of 3418A is higher than that of DTP. Therefore, the interaction of chalcopyrite with 3418A is stronger than with DTP.