Abstract: A comprehensive insight into the evolution and molecular structure of basic and neutral nitrogen compounds during the residue hydrotreating (RHT) process was gained through ESI(+)/ESI(−) FT-ICR MS analysis of the feedstock and its hydrogenated samples, with hydrodenitrogenation (HDN) ratios of 15.9%–70.1%. This study revealed that carbazoles, characterized by a double bond equivalent (DBE) of 9–11, were the refractory neutral nitrogen compounds during the RHT process. Their recalcitrant nature was primarily due to their low aromaticity and high steric hindrance. Conversely, quinolines (DBEs 7 to 9) were the most abundant basic nitrogen compounds. Through a meticulous analysis of DBE evolution, we revealed the intricate reaction mechanisms of benzocarbazoles and dibenzocarbazoles in residual oil, highlighting the crucial role of quinolines as key intermediates in eliminating these compounds. Interestingly, nitrogen compounds with either low or high carbon numbers (for a given DBE) exhibited higher reactivity than those with medium carbon numbers, which can be attributed to the low steric hindrance resulting from short alkyl chains and more naphthenic-aromatic structures, respectively. After hydrotreatment, the molecular structures of the most refractory or abundant nitrogen compounds could consist of two main types: those with multiple naphthenic-aromatic rings and those with long side chains near the nitrogen atom. This research has revealed nitrogen compounds' evolutionary mechanisms and refractory nature, and the molecular structure of the most resistant or abundant basic and neutral nitrogen compounds, providing a deeper understanding of the HDN process and ultimately paving the way for the rational RHT catalyst design and process development.