Perfluorinated sulfonic acid (PFSA) ionomers are the most widely used solid electrolyte in electrochemical technologies due to their remarkable ionic conductivity with simultanous mechanical stability, imparted by their phase-separated morphology. In this work, the morphology and swelling of PFSA ionomers (Nafion and 3M) as bulk membranes (>10 μm) and dispersion-cast thin films (<100 nm) are investigated to identify the roles of equivalent weight (EW) and side-chain length across lengthscales. Humidity-dependent structural changes as well as different PFSA chemistries are explored in the thin-film regime, allowing for the development of thickness-EW phase diagrams. The ratio of macroscopic (thickness) to nanoscopic (domain spacing) swelling during hydration is found to be affine (1:1) in thin films, but increases as the thickness approaches bulk values, revealing the existence of a mesoscale organization governing the multiscale swelling in PFSAs. Ionomer chemistry, in particular EW, is found to play a key role in altering the confinement-driven structural changes, including thin-film anisotropy, with phase separation becoming weaker as the film thickness is reduced below 25 nm or as EW is increased. For the lower-EW 3M PFSA ionomers, confinement appears to induce even stronger phase separation accompanied by domain alignment parallel to the substrate.