We built a molecular-level kinetic model for hydrocarbon catalytic cracking, incorporating the catalyst acidity as the parameter to estimate the reaction rates. The n-decane and 1-hexene co-conversion catalytic cracking process was chosen as the studying case. The reaction network was automatically generated with a computer-aided algorithm. A modified linear free energy relationship was proposed to estimate the activation energy in a complex reaction system. The kinetic parameters were initially regressed from the experimental data under various reaction conditions. On this basis, the product composition was evaluated for three catalytic cracking catalysts with different Si/Al. The Bronsted acid and Lewis acid as the key catalyst properties were correlated with the kinetic parameters. The built model can calculate the product distribution, and molecular composition at different reaction conditions for different catalysts. The sensitive study shows that it will facilitate the model-based optimization of catalysts and reaction conditions according to product demands.