We have investigated changes of proton channel network in Nafion membranes annealed at elevated temperatures using current sensing atomic force microscopy aimed at understanding the aging process of the membranes. The results reveal that the changes of proton channel network undergo two steps: First, the configuration of the ionic domains on the membrane surface changes from cluster-like to chain-like structure, accompanied by an increase of the proton conductivity of the membrane. As the annealing continues, the chain-like configuration for the proton channels persists but the conductance of the membranes decreases. The time constant of the conductivity decay decreases with the annealing temperature. The observed changes can be explained in terms of reorientation of proton channels near the membrane surface from perpendicular to parallel to the surface as the annealing temperature approaches the glass transition of the membranes.