Phenazines, as a type of electron shuttle, are involved in various biological processes to facilitate microbial energy metabolism and electron transfer. They constitute a large group of nitrogen-containing heterocyclic compounds, which can be produced by a diverse range of bacteria or by artificial synthesis. They vary significantly in their properties, depending mainly on the nature and position of substitutent group. Thus, it is of great interest to find out the most favorable substituent type and molecular structure of phenazines for electron transfer routes. Here, the impacts of the substituent group on the reduction potentials of phenazine-type redox mediators in aqueous solution were investigated by quantum chemical calculations, and the calculation results were further validated with experimental data. The results show that the reaction free energy was substantially affected by the location of substituent groups on the phenazine molecule and the protonated water clusters. For the main proton addition process, the phenazines substituted with electron-donating groups and those with electron-withdrawing groups interacted with different protonated water clusters, attributed to the proximity effect of water molecules on proton transfer. Thus, high energy conversion efficiency could be achieved by controlling electron flow route with appropriate substituted phenazines to reduce the biological energy acquisition. This study provides useful information for designing efficient redox mediators to promote electron transfer between microbes and terminal acceptors, which are essential to bioenergy recovery from wastes and environmental bioremediation.