Positive-ion mode of atmospheric pressure photoionization (APPI) coupled with a 9.4 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer has been applied to the characterization of shale oil from pyrolysis and its hydrotreatment. The hydrotreated shale oil was obtained through reactions over catalysts Ni-Mo, Ni-W, or Co-Mo. It was found that N-1 and N1O1 species are the dominant N compounds and Si species is the dominant S compound in shale oil from pyrolyzing Huadian oil shale. The primary aromatic hydrocarbons (AHCs) are mono- and double-ring aromatics. After hydrotreatment, both S and N compounds are effectively removed and the catalyst Ni-Mo shows the best performance in hydrodesulfurization (HDS) and hydrodenitrogenation (HDN). The AHC species, especially the mono-ring aromatics, increases as a result of the transformation of N-1, N1O1, and S-1 species into AHC species through hydrotreatment. Indole, carbazole, acridine, and their derivatives are preserved as N-1 species. The reactions of HDN for shale oil were further analyzed by considering the transformation between N1O1 and N-1 species.