The physical integrity of perfluorosulfonic acid (PFSA) ionomer membranes for fuel cell application depends on their internal morphology and distribution of hydrophilic and hydrophobic phases. Here, contrast enhanced transmission electron microscope-tomography (TEM-t) of pristine and degraded PFSA ionomer membranes is carried out to explore the effects of degradation in operating fuel cells. Nanoscale 3-D image reconstruction followed by Marker-based Watershed segmentation is used to identify weak phase boundaries in the tomograms and thereby reveal the hydrophilic and hydrophobic phase distributions in the membrane. The pristine membrane exhibits a randomly interconnected hydrophilic phase with a scaffolding hydrophobic phase, as expected from morphological theory. The degraded membrane subjected to combined chemical/mechanical degradation is found to have similar overall morphology while containing thinner ionomer bundles and reduced hydrophilic volume fraction with smaller hydrophilic pores in regions with elevated chemical degradation. Numerical analysis of the phase-segmented tomograms enables detailed quantification of the structural properties, as reported herein, which is not possible with 2-D approaches and therefore contributes important new information for nanoscale analysis of fuel cell membranes.