To investigate the effect of Fe(II/III) doping on the microscopic mechanism of methylamine salt hydrophobic modifiers on kaolinite surfaces, the adsorption characteristics of various methylamine cations on Fe(II/III)-doped kaolinite (denoted as Fe(II/III)-Kao) surfaces are calculated by density functional theory (DFT). The simulation results, including the Fukui index, adsorption energy, Mulliken bond populations, and charge analysis, reveal that Fe(II/III) doping enhances the surface activity of kaolinite, with significant effects observed in proximity to the doping site. Consequently, Fe(II/III) doping strengthens the interaction between methylamine cations and kaolinite surfaces. The adsorption mechanism of various methylamine cations on Fe(II/III)-Kao surfaces is attributed to a combination of hydrogen bonding and electrostatic attraction, with electrostatic attraction dominating the adsorption process. By comparing the adsorption energy of methylamine cations and alkyl carbon chains on Fe(II/III)-Kao surfaces, it becomes evident that the alkyl carbon chain has minimal impact on the adsorption of the hydrophobic modifier on Fe(II/III)-Kao surfaces. This finding confirms that the ammonium salt hydrophobic modifier primarily adsorbs onto Fe(II/III)-Kao surfaces through its polar head groups. The research results establish a theoretical foundation for further investigations on fine clay particle interface control and hydrophobic modifier design, ultimately guiding practical production processes.