In the realm of environmental science, it is of the utmost importance to derive clean energy from fossil fuel stock. The primary goal of this review article is to inspect key barriers to the increase use of liquid fuels in the transportation sector. The combustion of transportation fuel releases a more significant number of air pollutants into the atmosphere, with sulfurous and carbonaceous species particularly damaging the environment and causing human health problems. Desulfurization, in this dynamic industry makes a significant contribution by removing sulfur compounds, ensuring the efficient utilization of fuels without the emission of harmful sulfur oxides (SOX emissions). Additionally, to minimize such pollutants, the Environmental Protection Agency (EPA) enacted strict regulations that mandate an ultra-low desulfurization process to comply with the sulfur standard. However, choosing a more appropriate and efficient catalyst has always been a challenge. Moreover, using our critical evaluation, inorganic hybrid molybdenum (Mo) based materials have significant role for both conventional and non-conventional technologies. The factors which can influence the activity of desulfurization catalysts such as temperature, solvent, and concentration are more clearly outlined. With this outline, herein, the current industrial techniques such as hydrodynamic cavity method and coupled desulfurization technologies have been proposed. Moreover, we highlight the technical challenges and scalability while adopting a particular method and address solutions based on contemporary advances. The present review article is expected to provide a clear and systematic understanding on the design and development of active catalysts for various desulfurization technologies. In the concluding section, the prospects and limitations for various Mo based catalysts are thoroughly summarized.