Hydrodenitrogenation (HDN) is still a challenging process that many refineries need to overcome. The influence of catalysts on HDN efficiency cannot be ignored. In this study, Qilu atmospheric residue was subjected to a pilot-scale continuous hydrotreater, and liquid products were obtained from four outlets under two typical catalyst gradations. Basic nitrogen (BN) and non-basic nitrogen (NBN) compounds in the feedstock and liquid products were investigated by positive and negative (±) electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry. It shows that during hydrotreating, compared to BN, NBN compounds were more refractory. The removal of multi-heteroatom compounds occurred mainly in BN compounds, and the conversion of multi-heteroatom compounds and the hydrodearomatization of N1 class species happened simultaneously in NBN compounds. By comparing the effects of two typical catalyst gradations on the products, it was clear that in the removal of N1 class species, catalyst gradations had subtle differences. The significant difference in N removal efficiency was reflected in removal and transformation of N-containing compounds containing multiple heteroatoms in both BN and NBN compounds during the refining section. This observation provides a new contribution to understanding the use of different catalyst gradations in the beds and the effect of each catalyst on the resulting liquid products.