2-methylthiophene (2 MT) and 3-methylthiophene (3 MT) are two pollutants that are not removed through the usual purification in the gas refineries and lead to the release of SOX after combustion. A novel active hierarchical architecture of Fe2O3 hollow nanospindle coated by polyaniline-Zinc(II)-substituted α-Keggin type polyoxotungestate (Fe2O3NHS@PA/αSiW11Zn composites) is presented for removal of 2-methylthiophene (2 MT) and 3-methylthiophene (3 MT) as representative of alkylthiophenes. In this research, using a combined method based on simultaneous extraction techniques, 99.1% of 2 MT and 98.7% of 3 MT were successfully removed. The process involves the simultaneous use of ultrasound-assisted extraction phenomenon by an ionic liquid and catalytic oxidation by the heterogeneous hybrid nanocatalyst (UA-ECODS). The advantages of this process include the possibility of producing ultra-clean fuels, mild operational conditions, and cost-effectiveness. For this purpose, Box-Behnken Design (BBD) and response surface methodology (RSM) were used to design experiments and study the parameters. The affecting factors were optimized in terms of removal efficiencies by response surface methodology. The oxidation progress was studied more closely based on a pseudo-first-order kinetic model at different temperatures for various ultrasonic times. The Fe2O3NHS@PA/αSiW11Zn nanocomposite can be used as an efficient and recyclable phase-transfer heterogeneous catalyst to remove mercaptans from gas refinery products.