The deep desulfurization of oil fraction is a central matter of concern to every refinery. Hydrogen sulfide is the product of hydrodesulfurization reaction and it is the inhibiter of the reaction. When products inhibit the reaction, the counter-current operation is expected to have an advantage over the co-current operation. Hydrodesulfurization of vacuum gas oil in a trickle bed reactor was simulated for both models of co-current operation and counter-current operation. The models were simulated on high and low gas and liquid velocities. Hydrogen sulfide was affected by mass transfer resistance in both gas-liquid and liquid-catalyst interface. The other component mass transfer resistances were negligible. When the deep desulfurization was required, simulation results showed that the counter-current operation was superior to the co-current operation in organic sulfur conversion.