Molecular dynamics method is used to investigate the mass transfer rules of reactants H3O+ and O-2 in the cathode catalyst layer in the presence of five kinds of cations (Na+, K+, NH4+, Mg2+, Ca2+) in the microbial fuel cell solution environment. Structural characteristics of the catalyst layer Pt/C substrate/Nafion/solution three-phase interface are also analyzed. The results show that the transport mechanism and pathway of H3O+ in the catalyst layer are similar to those of monovalent cations (Na+, K+, NH4+). The minimum diffusion coefficient of H3O+ appears in the presence of K+. On the other hand, H3O+ mainly transport inside the water clusters in the presence of divalent cations (Mg2+, Ca2+). The diffusion law of metal cations (K+ > Na+ > Mg2+ > Ca2+) is still applicable in the catalyst layer containing Nafion ionomer and unaffected by cation concentration. In general, the higher concentration of O-2 molecules in the main part of the Nafion phase and the farther distribution from the carbon substrate cause a larger O-2 diffusion coefficient. Moreover, the O-2 transport pathways in the main part of the Nafion phase are along the Nafion hydrophilic/hydrophobic phase interface and inside the hydrophobic phase. In the presence of Ca2+, the concentration of O-2 near the Pt particles is the highest. These O-2 molecules tend to adsorb on the surface of Pt particles with small size. Thus, the catalyst utilization rate is high. In addition, Ca2+ has a strong cross-linking effect on the sulfonic acid groups from different Nafion molecules, which helps to enhance the stability of the catalyst layer. (C) 2019 Elsevier Ltd. All rights reserved.