In this research, kaolinite was used to investigate the comparative adsorption of copper, lead, and zinc ions through batch control experiments and first principles calculations. Different adsorption conditions were considered as the effect of solution acidity, initial concentration of ions, and contact shaking time. The adsorption system isotherms and kinetic studies were better agreed with the Langmuir and pseudo-second-order kinetic models. They reached adsorption equilibrium within two hours and maximum adsorption capacities of Zn(II), Pb(II), and Cu(II) on kaolinite were 15.515, 61.523, and 44.659 mg/g, respectively. In addition, the microscopic adsorption changes of Zn(II), Pb(II), and Cu(II) on kaolinite were characterized using X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron microscopy with energy dispersive X-ray spectroscopy. The results showed that Zn(II), Pb(II), and Cu(II) were most likely to be adsorbed on the kaolinite surface. Furthermore, the adsorption mechanism of [Zn(OH)]+, [Pb(OH)]+, and [Cu(OH)]+ on the kaolinite (001) surface was systematically studied through first-principles density functional calculations. The adsorption characteristics of different ions were evaluated by calculating the adsorption energy of the equilibrium adsorption configuration, state density, and electron density. The adsorption energy of [Zn(OH)]+, [Pb(OH)]+, and [Cu(OH)]+ were − 0.49, − 1.17, and − 1.64 eV, respectively. The simulation results indicated that new hybrid orbitals were formed between the metal ions and O atoms on the kaolinite surface, with electron transfer occurring the adsorption processes. The charge transfer direction for [Pb(OH)]+ was opposite those for [Zn(OH)]+ and [Cu(OH)]+. [Zn(OH)]+ was more likely to form polydentate complexes with hydroxyl groups on the kaolinite surface than [Cu(OH)]+ and [Pb(OH)]+. This work further elucidated the interaction mechanism between the adsorption systems and provided fundamental theoretical support for the structural modification and optimization of kaolinite, such as increasing the layer spacing of kaolinite and introducing other active groups on its surface to improve the adsorption capacity of heavy metal ions in water treatment and soil remediation.