This work focuses on the preparation, simulation, and optimization of the hydrodesulfurization (HDS) of dibenzothiophene (DBT) using a nanocatalyst. A homemade nanocatalyst (3 percent Co, 10 percent Mo/γ-Al2O3 nanoparticles) was used in a trickle bed reactor (TBR). The HDS kinetic model was estimated based on experimental observations over ranges of operating conditions to evaluate kinetic parameters of the HDS process and apply the key parameters. Based on these parameters, the performance of the TBR catalyzed by the nanocatalyst was evaluated and scaled up to a commercial scale. Also, the selectivity of HDS reactions was also modeled to achieve the highest yield of the desired hydrogenation product based on the desirable route of HDS. A comprehensive modeling and simulation of the HDS process in a TBR was developed and the output results were compared with experimental results. The comparison showed that the simulated and experimental data of the HDS process match well with a standard error of up to 5%. The best reaction kinetic variables obtained from the HDS pilot-plant (specific reaction rate expression, rate law, and selectivity) TBR have been utilized to develop an industrial scale HDS of DBT. The hydrodynamic key factors (effect of radial and axial dispersion) were employed to obtain the ratio of the optimal working reactor residence time to reactor diameter.