The rapid advances in mass spectrometry and related technologies in the last two decades have revolutionized our understanding of heavy petroleum composition and greatly accelerated research and development within the oil and gas industry. Petroleum is a highly complex mixture of hydrocarbons and heteroatom-containing (S, N, O, metals, and more) hydrocarbons. Molecular composition has a significant impact on the properties of crude oils and the way they need to be handled in refining processes. In this review, the current state is highlighted, as well as progress in key areas of the molecular characterization of heavy petroleum, including separation approaches, ionization methods, high-resolution mass spectrometry, dissociation technology, and multidimensional separation mass spectrometry, including GC soft ionization mass spectrometry and ion mobility-mass spectrometry.