The catalyst for diesel ultra-deep desulfurization is selected on the basis of several factors, including feedstock composition, liquid hourly space velocity, and operation pressure. Owing to their specific processing purposes, different catalyst systems, such as straight distillation, coking distillation, blends of straight distillation, and secondary processing oil, are applied for various feeds because of their considerable difference in terms of sulfur content, nitrogen content, aromatics constitute, and cetane number. This study aims to determine the most appropriate catalyst and grading scheme by evaluating the deep desulfurization efficiency of different schemes when processing various feeds. The results showed that the W-MoNi/Mo-Co catalyst stacking is the most effective among various schemes because of the following reasons: (1) loading W-Mo-Ni catalyst on the upper bed of reactor not only benefits the saturation of polyaromatics even in the middle or at the end of the run but also provides low nitrogen feed for the bottom bed; (2) loading Mo-Co type catalyst with alkyl transfer performance in the bottom bed at high temperature reaction zone facilitates alkyl transfer reaction and mitigates the effect of thermodynamic equilibrium limitations in the middle and at the end of the run, consequently improving the HDS efficiency under high temperatures.