The improvement of fuel quality requires the reduction of sulfur content. The main challenge of catalytic cracking diesel extraction desulfurization is to find low-price and good-performance extractants. Based on experimental research, this work further explores the separation mechanism of DES for thiophene (TP) and benzothiophene (BTP). First, the COSMOS-RS model was used to predict the separation performance of 10 HBAs and 10 HBDs for TP and BTP. The results showed that the low-cost carboxylic acid based DES had excellent separation performance. Secondly, the effect of experimental conditions on the separation performance of three carboxylic acid based DESs was investigated. When the molar ratio of DES to TP and BTP was 3:1, after three stage extraction, the extraction rates of TP and BTP by TEAC: PrA(1:3) were 98.06 % and 98.53 %, respectively. Finally, the structure–activity relationship was studied by using quantum chemistry and molecular dynamics simulation. It was found that EvdW plays a dominant role in the desulfurization process and does not include H-bond interactions. TEA+ was distributed parallel to the aromatic ring and has a CH···π interaction with thiophene. TP and BTP were distributed in the voids of DES and do not affect the regeneration performance of DES.