Adsorbent material was prepared using distillers’ grains (DG), which is a waste product of distilleries. The DG was pre-treated with NaOH and esterification-modified with CS2, which is a commonly used anionic modifier. The structure and morphology of the adsorbent was characterized by FTIR, XRD, EDS, SEM, BET, and zeta potential. The related mechanism of adsorption of malachite green (MG) onto modified distiller’s grains (MDG) was studied by adsorption experiments and molecular simulation techniques. The experimental results showed that CS2 successfully modified the DG fiber, and simultaneously yielded the MDG with a uniform pore distribution. MDG had a considerable adsorption capacity of 367.39 mg/g and a maximum removal rate of 96.51%. After eight adsorption–desorption cycle experiments, the adsorption removal rate of MDG to MG dye remained at 82.6%. The adsorption process could be fitted well by a pseudo-second-order kinetic model (the correlation coefficient R2 > 0.998) and Freundlich isotherm adsorption equation (the correlation coefficient R2 > 0.972). Moreover, the adsorption of MG dye by MDG is a spontaneous, endothermic, and increased entropy process. The results of molecular simulation showed that the mechanism of MG molecules onto MDG was mainly chemical adsorption. The adsorption performance of MG onto MDG was better and more stable than DG. Molecular simulation also provided a theoretical guidance of MDG adsorption–desorption for the research on recycling of DG resources.