The acidity and pore structure of zeolite catalysts play a crucial role in the selectivity and stability of C4 alkylation due to the synergistic effect of reaction activity and diffusion. Herein, the effect of three acidic beta zeolites with different Si/Al ratios on adsorption, diffusion, and catalytic performance was studied using experiments and molecular simulations. The beta zeolite with the lower Si/Al ratio leads to the faster relative diffusion of isobutane to 1-butene and the smaller adsorption amount of alkylate products. Furthermore, the diffusion of molecules in the zigzag channel along the z direction of beta zeolites is much slower than other two directions. The experimental results indicate that lower Si/Al ratio cause the higher content of strong BAS in the zeolite, resulting in the higher hydride activity and the longer catalytic lifetime. This work provides a theoretical basis for the development of high catalytic activity zeolite catalysts.