The tighter specifications for refining products have gradually led refineries to focus on the molecular modeling of petroleum processing. In this work, a systematic methodology is presented for the molecular modeling of heavy oil thermal cracking (HOTC). This research which is based on a microscopic understanding provides a basis to achieve better design, management, optimization, and control of HOTC. The molecular information of HOTC product streams is represented in the form of a MTHS (molecular type homologous series) matrix. From consideration of the complexity of structural isomers in heavy petroleum fractions, the heavy molecules in a homologous series are grouped to reduce the dimension of the MTHS matrix. Transformation correlations are developed to capture the molecular properties of each homologous series in the MTHS matrix and to interrelate the molecular composition and bulk properties of the product streams. The HOTC process model was built on the basis of the molecular representation provided by the MTHS matrix and the transformation correlations. Two case studies are illustrated for validation of the proposed model and methodology.