The simultaneous occurrence of reaction and diffusion in zeolite presents a challenge in distinguishing their individual effects through experimental means. While simulations can provide free energy profiles for diffusion and reaction, they offer predictions of product distributions only in the equilibrium state. However, the limited zeolite volume and molecule retention time can lead to deviations from the equilibrium concentration in the actual product distribution. In this study, the free energy barriers are integrated with kinetic Monte Carlo simulations, and the reliability of the model is validated through comparison with experimental results. Subsequently, the impact of xylene occupancy, Si/Al ratio, and zeolite morphology on the PX selectivity is further investigated. The findings reveal that twin HZSM-5 with zigzag channels predominantly opened to its external surface serves as an outstanding catalyst capable of maintaining high PX selectivity across a wide range of xylene occupancy. Additionally, HZSM-5 nanosheet crystals with a zigzag channel as the minor axis exhibit high PX selectivity while significantly reducing the diffusion distance, thereby slowing the deactivation rate. These results collectively indicate that this approach introduces novel concepts for improved quantitative prediction of catalyst performance.