Methyl Violet (MV) was removed from aqueous solutions by adsorption onto halloysite nanoclay (HNC) employing equilibrium, kinetics, thermodynamic data, molecular modellingR (MD), and Monte Carlo (MC) simulations. The chosen experimental variables were pH, temperature, starting MV concentration, contact time, and adsorbent dosage. The adsorption rate was determined to increase with increasing contact time, initial dye concentration, pH, and temperature. The Langmuir, Freundlich, Temkin, and Dubinin–Radushkevich (D-R) isotherms were utilized to determine the adsorption capacity of HNC. The Langmuir equation matched equilibrium data better than the other models, whereas the pseudo-second-order model better described kinetic data, and thermodynamic analyses revealed that the adsorption process was spontaneous, endothermic, and physisorption-based. This study focused on two distinct molecular mechanics-based theoretical approaches (MC and MD). These techniques enabled a molecular comprehension of the interaction between the MV molecule and the halloysite surface. Theoretical results were consistent with experimental findings. The outcomes revealed that HNC is an excellent dye adsorbent for industrial effluents.