Based on the structure-oriented lumping method, a molecular-level reaction kinetic model of the delayed coking process, which adopted 24 structural increments to construct the feed molecular matrix containing 2,944 molecules, was established with a reaction network containing 74,581 reactions using MATLAB. The reliability of the model was verified by experimental results. According to the discriminant rules of structural increments, 173 structural vectors in gasoline and 1,132 structural vectors in diesel were classified into different group compositions, respectively. The model could track the reaction path of any specific molecule in the complex thermal cracking reaction network. The influences of operation conditions such as recycle ratio on the product distribution could be discovered through the calculation of the molecular-level model, which is helpful for the process optimization and precise regulation of product composition for the delayed coking plants.