During combustion, sulfur compounds in fuels are oxidized to SO x , poisoning automatic catalytic converters and posing severe environmental risks (e.g., acid rain). As an outcome, effective liquid fuel desulphurization is a vital step in reducing SO x emissions and their inherent ecological impacts. The extraction of ultralow benzothiophene from n-decane as representative model diesel fuel was analyzed using phosphonium-based deep eutectic solvents (DESs) at 308.15 K and 1 bar pressure. Liquid−liquid equilibrium (LLE) studies were conducted on a ternary system of DES− benzothiophene−n-decane for all six feed point concentrations. 1 H NMR analysis was used to determine the molar composition of each raffinate and extract phase. The LLE experimental findings were examined using a conductor-like screening model for segment activity coefficient (COSMO-SAC) based on quantum calculations. The average root-mean-square deviation (RMSD) of the studied LLE ternary system was 1.07%, which was suitable considering the prior nature of the approach. The σ-profile calculations using the COSMO-SAC model and Hansen solubility parameters (HSPs) using different predicted models were used to provide insights into the molecular mechanism of benzothiophene extraction efficacy using DES. We observed higher extraction of benzothiophene due to the higher proportion of hydrogen-bonding and dispersion-type interactions. Charge transfer analysis using the density functional theory (DFT) calculation of the DES cluster suggested that bromide (Br − ) ions can act as a charge transfer bridge between the methyltriphenylphosphonium (MTP) cation and the hydrogen bond donor. The MTP cation and ethylene glycol also aided in the extraction of benzothiophene by dislocating charge from the aromatic sulfur compound. The bromide (Br − ) ion is essentially noninteractive with benzothiophene due to retention of the conventional hydrogen bond network existing within the initial components of DES, mainly hydrogen bond donors and hydrogen bond acceptors.