When studying the evolution of refractory species during hydrotreatment, the polyheteroatomic compounds containing both nitrogen and sulfur or nitrogen and oxygen atoms are sometimes neglected. However, even a low amount of these compounds could reduce the efficiency of the removal of N1 or S1 compounds, which is the main target of hydrotreatment. In this paper, three different vacuum gas oil feedstocks were analyzed along with their corresponding hydrotreated samples using electrospray ionization (ESI(+) and ESI(-)) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analyses. The evolution of the aromaticity and the alkylation of the polyheteroatomic compounds during hydrotreatment were followed using double bond equivalent (DBE) versus the number of carbon atoms (DBE = f(#C) plots). Moreover, as the hydrotreated samples were produced using the same operating conditions, the reactivity of the different feeds has been assessed. Finally, an additional hydrotreated sample was produced using a higher temperature and analyzed, allowing us to monitor the impact of temperature on the removal of the heteroatomic species. From a general point of view, basic polyheteroatomic species are more refractory than neutral or acidic polyheteroatomic species. It has also been shown that depending on the heteroatomic class considered, the hydrotreated samples could exhibit different aromaticity and alkylation distributions, whereas the distributions of the feeds were similar, which is characteristic of different hydrotreatment mechanisms. Finally, the positive impact of higher operating temperature on the removal of most of the species but in different ratios has been clearly demonstrated. This study takes advantage of FT-ICR MS to monitor the evolution of refractory species during hydrotreatment as well as being a powerful tool to put forward the reactivity differences between several feedstocks or study the impact of hydrotreatment operating conditions.