In this work, molecular-level kinetic modeling was developed for the fluid catalytic pyrolysis of straight-run naphtha based on the structural unit and bond-electron matrix framework. The kinetic parameters were tuned and optimized using systematic experimental data from a fluidized bed under different conditions, the predicted values of the fraction yield, naphtha composition, and gas product yield were in agreement with the experimental data. The model can obtain the typical reaction rate of naphtha with different carbon numbers and structure compositions at the molecular level under typical conditions. The model can also quantify and compare the effects of eliminating different side reactions on the light olefins production, and different optimized reaction types of naphtha feedstocks under two typical conditions were revealed, quantitative model calculations show a significant boost in light olefin yield of 15–33 percentage points without hydrogen transfer.