Two clay minerals, kaolinite (Kaol) and montmorillonite (Mt) with different crystal structures were chosen to investigate the comparative adsorption of 2-phosphonobutane-1,2,4-tricarboxylic acid (PBTC) through batch control experiments and theoretical studies. The systematical isotherm and kinetic studies agreed with Langmuir model and pseudo-second-order model, confirming a monolayer and chemisorption interaction process, respectively. The maximum removal capacities of Kaol and Mt for PBTC were 72.297 mg/g and 121.163 mg/g at pH=3.0 and T=298 K, respectively. Furthermore, the adsorption mechanisms were investigated by molecular dynamic (MD) simulations and density functional theory (DFT). The Interface force field (IFF) was firstly introduced into Materials Studio package to explore the microscopic mechanism of clay mineral interface. The dynamics behaviors verified that the oxygen (O) atom of carboxyl group has stronger affinity at the external surface of Mt, which consistent with the experimental data well. For DFT calculations, quantitative analysis around molecular van der Waals (vdW) surface was adopted to predict reactive sites for the electrophilic reaction. Independent Gradient Model (IGM) and Hirshfeld surface analyses in Multiwfn indicated that the high adsorption effect mainly attributes to hydrogen bond action. These findings improve our ability to explore the related properties occurring at the interface of different clay minerals.