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 N-1 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 N-1 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.