The low effectiveness factor of catalyst pellet caused by high internal diffusion limitation is a common issue in fixed-bed reactor. Nevertheless, hierarchical structured catalyst provides a promising solution for the contradiction between reaction activity and diffusion efficiency in large catalyst pellets. Herein, we studied the effect of pore structure parameters of the meso-macroporous catalyst on Fischer-Tropsch synthesis performances through experiment and pellet scale reaction-diffusion simulation. The pellet simulation firstly elucidated the reason for the significant improvement on activity and product selectivity for the meso-macroporous catalyst observed in our experiment. Further optimization via pellet simulation indicated the critical influences of wax filling degree and that the perfect matching between reaction and mass transfer rates by increasing macropore size and adjusting porosity within pellet enables the C5+ space-time yield to the maximum. This work could provide a theoretical guideline for the engineering design of the hierarchical structured catalyst pellet.