Atmospheric residue (AR) from Saudi Arabia (SZAR) was subjected to supercritical fluid extraction fractionation (SFEF) and four extractable subfractions (SFEF-1-4) and an unextractable end-cut were obtained. SZAR and SFEF-1-4 were subjected to hydrotreatment (HDT) in a continuous mini fixed-bed reactor. Three commercial catalysts were used to remove the impurity in the feedstock. The composition and structural transformation of nitrogen (N)-containing compounds were investigated. Electrospray ionization (ESI) Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) was used for molecular characterization of N-containing compounds of SZAR, extractable SFEF subfractions, and HDT products. Results showed that N-1 class species with high aromaticity and/or low carbon number exhibited higher catalytic hydrogenation reactivity. N-1 class species with lower aromaticity were removed regardless of chain length.