In this presented work, a heavy petroleum fluid catalytic cracking (FCC) process model based on the use of a hybrid structural unit and bond‐electron matrix (SU‐BEM) framework on a molecular level has been developed. The SU‐BEM uses a simplified structural unit to represent the petroleum's molecular structure and chemical conversion, while retaining substantial details regarding atom‐connectivity. The chemical reaction information from the FCC unit was characterized in terms of reaction rules, indicating the conversion between structural units. After implementing via iteration the reaction rules on feedstock molecules, a complex molecular reaction network was created, containing all the primary product molecules (~3,800) and the reactions (~7,500). Next, the process mathematical model was built, including the micro‐kinetic model and the FCC unit reactor model. For validation purposes, the product yield was selected as a predicted variable. Following a parameter estimation procedure, a good agreement between the calculated and experimental values was observed.