The molecular structure of cationic surfactants is closely related to their flotation performance. In this paper, three cationic surfactants with different head group structures were selected as collectors of kaolinite, and the substituent effects were studied by the DFT method. The DFT calculation results showed that increasing the number of substituents in the dodecylamine head group can significantly increase its surface and head group charge. Dodecylamine has the lowest LUMO orbital energy, so dodecylamine has the strongest electron attraction ability and the strongest interaction with kaolinite. Electron density differential showed that there was an area of electron aggregation between the collector and the surface of the kaolinite. The interaction energy of DDA on kaolinite surfaces was greater than that of the other two collectors, indicating that the adsorption of DDA on the surface of kaolinite was more stable. Flotation results showed that higher a kaolinite yield was obtained in the presence of dodecyl dihydroxyethyl methyl ammonium chloride. The calculated results of the solvent-accessible surfaces, the head group charge, and the number of bonds between the collector and the kaolinite show good consistency with the actual flotation results of the three collectors, which can be used as a screening index for kaolinite flotation collectors.