In this study, we investigate aqueous proton penetration behavior across four types of two-dimensional (2D) nanoporous materials with similar pore sizes using extensive ReaxFF molecular dynamics simulations. The results reveal significant differences in proton penetration energy barriers among the four kinds of 2D materials, despite their comparable pore sizes. Our analysis indicates that these variations in energy barriers stem from differences in the hydrogen bond (HB) network formed between the 2D nanoporous materials and the aqueous environment. The HB network can be classified into two categories: those formed between the surface of the 2D nanoporous materials and the aqueous environment, and those formed between the edge atoms of the nanopores and the water molecules inside the pores. A strong HB network formed between the surface of the 2D nanoporous materials and the aqueous environment induces an orientational preference of water molecules, resulting in an aggregated water layer with high density. This high-density water region traps protons, making it difficult for them to escape and penetrate the nanopores. On the other hand, a strong HB network formed between the edge atoms of the nanopores and the water molecules inside the pores impedes the rotation and migration of water molecules, further inhibiting proton penetration behavior. To facilitate the proton penetration process, in addition to a sufficiently large pore size, a weak HB network between the 2D nanoporous material and the aqueous environment is necessary.