In the catalytic layer of proton exchange membrane fuel cells, water molecules in ionomers tend to be accumulated at the ionomer/Pt interface, preventing oxygen from reaching the Pt surface to participate in chemical reactions. It is necessary to take measures to improve the water molecules distribution and proton transport performance in the ionomer on the Pt surface. In this work, the effect of “acid–base pair” functionalized graphene oxide (AB-GO) as the additive on the distribution of water molecules and transport property in the ionomer is evaluated. The results demonstrate that with the addition of AB-GO, the distribution uniformity of water molecules and hydronium ions in the ionomer on the Pt surface is improved. The connectivity of water cluster is also increased. When the doping ratio of BAF-GO and TF-GO is 1:3, the connectivity coefficient of water cluster is about 1.37 times that of Nafion ionomer without the doping.