Better understanding of the changes in composition and molecular structures of atmospheric residue (AR) during hydrotreating is important for improving the hydrotreating performance of AR Hydrotreating of an AR was carried out in a series of fixed bed reactors loaded with hydrodemetallization (HDM) and hydrodesulfurization (HDS) catalysts. The AR and its products were fractionated into saturates, aromatics, resins, and asphaltenes (SARA) and analyzed by using the gel permeation chromatography with an ultraviolet detector (GPC-UV) and with an inductively coupled plasma mass spectrometer (GPC), X-ray diffraction (XRD), C-13 nuclear magnetic resonance (C-13 NMR), and electron spin resonance (ESR). Hydrotreating not only decreased the contents of S, N, V, Ni, resins, and asphaltenes, but also changed the composition, structure, and distribution of the remaining resins and asphaltenes as well as the remaining S, N, V, and Ni compounds in AR products. Almost all metals (V and Ni) existed in both resin (47%) and asphaltene (53%) fractions of AR, whereas in the final hydrotreated product, more than 84% of the remaining metals, which are considered as the most refractory metal compounds, were in the asphaltenes, especially those with larger molecular size. The metal compounds in resins were easier to be removed. The low HDM reactivity of the remaining metal compounds can be attributed to their larger molecular size, which inhibited their approach to the active sites of the catalysts.