Our present work focused on the extractive distillation desulfurization from methyl tert-butyl ether (MTBE). By using dimethyl disulfide (DMDS) as the model compound contained in MTBE, the intermolecular interactions that happen among solvent, DMDS, and MTBE were analyzed and defined, and the interaction energies were calculated by applying density functional theory method. The interactions between solvents and DMDS are found to be van der Waals and weak hydrogen bond forces. The distributions of DMDS in solvents and MTBE also are calculated using dissipative particle dynamics. According to the computational results coupled with batch extractive distillation experiment using constant reflux ratio, dimethyl sulfoxide has the strongest interaction with DMDS and, therefore, exhibits the highest efficiency for DMDS removal. In addition, the reflux ratio-programmed batch extractive distillation (RRPED) process was developed. Under the suitable operation conditions of RRPED process, the sulfur content of product can be reduced from 2000 mu g/g to less than 5 mu g/g. The RRPED process was observed to achieve the largely enhanced desulfurization efficiency.