The development of high resolution mass spectrometry as well as other analytical techniques in the past decade enable the better characterization of complex chemical constituents of petroleum. This spawned a field which contemplates the relationship between the molecular composition of a petroleum feedstock and its properties and reactivity. Recently, “molecular refining” and “molecular management” were proposed and extensively discussed for designing and optimizing petroleum processing operations at the molecular level. Molecular refining involves the implementation of petroleomics in the downstream petroleum industry, whereas molecular management is the technical implementation of the idea of molecular refining. We define molecular management as the integrated technology solutions for beneficiating of the whole petroleum refining process based on the understanding of chemical composition at the molecular level. Molecular management techniques involve: (a) characterization and understanding of petroleum chemical composition at the molecular level; (b) revealing the correlation between molecular composition and physical properties of petroleum and its fractions/products; (c) predicting and controlling the destination and distribution of molecules in the blending and separation processes; (d) understanding the conversion mechanisms of the chemical refining processes; (e) realizing the modeling of molecular composition and process simulation and (f) applying the molecular composition based theoretical models to decision-making optimization, supply chain network optimization, and operation optimization throughout the entire the petroleum refining process. Three fundamental issues are introduced for the development of molecular management techniques: (1) the composition characterization based on instrumental analysis; (2) modeling of molecular composition and physical property prediction; (3) reaction network establishment and reaction kinetic parameters solution. Although significant progress has been achieved in the past decade in instrumental analysis, the compositional information from experiments still cannot completely meet the requirements of modeling development. The resolving power of mass spectrometry for heavy petroleum fractions and the ability to distinguish structural information of molecular isomers are the major challenges in the near future. For this reason, a molecule-based pseudo-component techniques a pragmatic approach to represent the feedstocks and products in petroleum refining process models. The modeling of molecular composition is critical for molecular management. Recently, physical property predication models have been successfully used for most petroleum fractions. One of the most significant challenges is to develop reaction models that include thousands of molecular components. More effort should be focused on the methodology and development of software tools for the automated construction, solution and optimization of detailed kinetic models. A brief overview of the development of the molecular management in petroleum refining and its prospects are also discussed.