Process synthesis is about finding the appropriate processing routes with selection of catalyst, reaction, and separation technologies followed by flowsheeting (connection of selected technologies) and equipment design at the least capital and operating cost. The common feature of the current process synthesis methods is that they are mainly based on macroscopic parameters but do not exploit microscopic effects at the molecular level. As a result, the fundamental aspects cannot be fully exploited to discover novel ideas. However, the essence of process synthesis is about maximizing the production of desirable chemical species via optimizing the routing of key species to their most appropriate destinations. To achieve this goal, a molecular analysis methodology for process synthesis is proposed in this article. Several industrial case studies are provided to prove the concept and demonstrate the value.