Deep-eutectic solvents (DES) have emerged as promising candidates for preparing nanocomposites. In this study, a DES-based graphitic carbon nitride (g-C3N4)/ZnO/Chitosan (Ch) nanocomposite was synthesized to remove malachite green (MG) dye from water. The DES was prepared by mixing and heating citric acid as a hydrogen bond acceptor and lactic acid as a hydrogen bond donor. This is the first report of the removal of MG using DES-based nanocomposites. Experiments on kinetics and isothermal adsorption were conducted to systematically explore the adsorption performances of nanocomposite toward dye. At 25 °C, the highest adsorption performance was obtained with alkaline media (>90 % removal). The greatest adsorption capacity (qm) was 59.52 mg g−1 at conditions (30 mg L−1 MG solution, pH 9, 3 mg nanocomposite per 10 mL of MG solution, 25 °C, 150 rpm, and 150 min) based on the calculation from the best-fitting isotherm model (Langmuir). The adsorption process was most appropriately kinetically described by the PSO model. The Monte Carlo (MC) and molecular dynamic (MC) results are correlated with experimental findings to validate the theoretical predictions and enhance the overall understanding of the adsorption process. Electronic structure calculations reveal the nature of interactions, including hydrogen bonding and electrostatic forces, between the nanocomposite and MG molecules.