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Understanding the adsorption behavior of antibiotic molecules on minerals is crucial for determining the environmental fate and transport of antibiotics in soils and waters. However, the microscopic mechanisms that govern the adsorption of common antibiotics, such as the molecular orientation during the adsorption process and the conformation of sorbate species, are not well understood. To address this gap, we conducted a series of molecular dynamics (MD) simulations and thermodynamics analyses to investigate the adsorption of two typical antibiotics, tetracycline (TET) and sulfathiazole (ST), on the surface of montmorillonite. The simulation results indicated that the adsorption free energy ranged from − 23 to − 32 kJ·mol−1, and − 9 to − 18 kJ·mol−1 for TET and ST, respectively, which was consistent with the measured difference of sorption coefficient (Kd) for TET-montmorillonite of 11.7 L·g−1 and ST-montmorillonite of 0.014 L·g−1. The simulations also found that TET was adsorbed through dimethylamino groups (85% in probability) with a molecular conformation vertical to the montmorillonite’s surface, while ST was adsorbed through sulfonyl amide group (95% in probability) with vertical, tilted and parallel conformations on the surface. The results confirmed that molecular spatial orientations could affect the adsorption capacity between antibiotics and minerals. Overall, the microscopic adsorption mechanisms revealed in this study provide critical insights into the complexities of antibiotics adsorption to soil and facilitate the prediction of adsorption capacity of antibiotics on minerals and their environmental transport and fate. This study contributes to our understanding of the environmental impacts of antibiotic usage and highlights the importance of considering molecular-level processes when assessing the fate and transport of antibiotics in the environment.