The aim of this paper is to identify the physical and chemical mechanism of ultrasound in presence of phase transfer agent (PTA) and phosphotungstic acid on desulfurization process. With different experimental procedures, we made an effort to identify the individual effect of phase transfer agent and ultrasound on oxidative desulfurization. Ultrasound-assisted process is the modern technique to enhance the kinetic of the liquid–liquid heterogeneous system. Physical and intrinsic properties of liquid fuels such as diffusivity of PTA-cation complex and also through effect on cavitation have a strong influence on Desulfurization of liquid fuels. Due to low vapor pressure of solvents, the beneficial effect of higher static pressure (that eliminates cavitation effect) is not seen in present reaction system. Phase transfer agent or phosphotungustic acid-assisted ultrasound desulfurization has radical and ionic reaction mechanism, which is revealed in terms of lower activation energy (energetic nature of radicals) as well as collision factor (due to instability of radicals) than magnetically stirred system. This study has revealed crucial mechanistic aspects of ultrasound assisted oxidative desulfurization in presence of phase transfer agent and phosphotungustic acid, which will give more insight for further research. © 2018 Curtin University and John Wiley & Sons, Ltd.