A new bentonite clay composite was synthesized by modifying bentonite clay and Schiff base (SB). The purpose of the composite was to eliminate methylene blue (MB) from wastewater. To characterize its efficacy, several spectroscopic techniques (UV-Visible spectroscopy, FTIR, SEM, and XRD) were used. The interactions between the adsorbent dose, pH, initial dye concentration, and contact duration were also tested to evaluate the adsorption capacity of the adsorbent. The results demonstrated that changes in the modification led to a considerable increase in adsorption capacity, with a maximum monolayer adsorption capacity of 258 mg/g being achieved at pH 11. Based on the batch experiments, molecular dynamics simulations, and DFT studies, the pseudo-second-order model described the sorption of MB on the bentonite clay composite the best. It was found that the adsorption of MB on the bentonite clay composite primarily followed a monolayer adsorption mechanism. Using the Langmuir isotherm model, the experimental results were consistent, indicating the monolayer adsorption mechanism. Finally, this study demonstrated that the bentonite-SB adsorbent had enormous promise for the elimination of methylene blue (MB) from wastewaters, as evidenced by the electron density mapping within the molecular electrostatic potential plot and the electrostatic potential graphing within the iso-surface plot.