In order to guide the accurate control of the sulfides in gasoline and diesel of Fluid Catalytic Cracking (FCC) process, a molecular-level model was established based on the Structure Oriented Lumping (SOL) method. According to the molecular composition characteristics of FCC feed oil, a molecular composition matrix containing 4,148 row vectors was constructed with 24 structural increments. Using MATLAB software, the SOL reaction rules were compiled and a complex reaction network containing of about 110,000 reactions was established. According to the classification rules, the sulfides in gasoline and diesel represented by 32 and 136 structural vectors were divided into mercaptans, thioethers, monocyclic thiophenes, benzothiophenes and dibenzothiophenes, respectively. The conversion law of sulfides in gasoline and diesel was investigated by tracking their generation paths and reaction paths in the reaction network. The effects of the operation conditions on the sulfide contents in gasoline and diesel were calculated quantitatively.