Most porous media (just like catalyst pellets) have complicated pore structures, and understanding the coupling of the diffusion and reaction processes in these pores is very important for improving their performance. In this work, a diffusion factor (D) and a reaction factor (R) are proposed to quantitatively describe the diffusion and reaction performance in these pores respectively at molecular level. The yield in unit time is used to quantify their productivity and is expressed as the product of D and R. Molecular dynamic simulations with the hard-sphere algorithm are carried out to study the reaction-diffusion coupling in several simple pore structures with the same volume, such as straight, T-shaped, and cross-shaped pores. The reaction formula based on activation energy is given for a simple irreversible reaction process from A to B. In terms of the proposed factors, D and R, analysis on the simulation results shows clearly that the overall productivity of these pore structures depends on the competition of D and R, which are both determined by the size and shape of the pore structures. The results demonstrate the effectiveness of the simulation approach used for evaluating the performance of the simple pore structures for simple reactions and the potential of its application in more complicated and practical cases. It also suggests the effectiveness of the proposed factors, D and R, for charactering the diffusion and reaction processes at molecular level.