We show that proton conductance variation in Nafion membranes can be mapped using current sensing atomic force microscopy (CSAFM) to reveal and to characterize the heterogeneity in proton transport properties of the membranes. The distribution obtained by using a conventional CSAFM probe tip coated with a catalyst layer on a fresh Nafion membrane under a humid condition always displays a Gaussian-like shape. Such a feature can be explained in terms of the size of the contact area between a CSAFM tip and the membrane in comparison to the size of the tip apex. The conductance of individual proton channels and the density of the channels can be derived from the distribution. The averaged conductance and the density of proton channels derived are found to be consistent with that obtained in a recent simulation work based on the small-angle X-ray scattering (SAXS) data.