Atmospheric residue from Saudi Arabia light crude oil was subjected to the hydrotreating process in a continuous fixed-bed reactor with hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) catalysts. The detailed molecular composition of the polar heteroatom species in the feedstock and products was determined by electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with other analytical methods. The ESI FT-ICR MS analysis indicates that the N1 class species have the highest relative abundance. In the hydrotreating process, small neutral N1 class species with high aromaticity and short side chains showed the highest relative abundance and were defined as easily removable compounds. High aromaticity and small molecule basic N1 compounds exhibited higher catalytic activity towards hydrogenation. The N1S1 class species were converted to the N1 class species, or even hydrocarbons, by the preferential removal of the sulfur atoms. Most of the N1O1 class species were difficult to remove, because of their stable chemical structure.