The focus of this dissertation was to investigate the influence of sidechain structure and sidechain content on the morphology and physical properties of perfluorosulfonic acid ionomer (PFSA) membranes. One of the primary objectives was to characterize the thermomechanical relaxations for short sidechain PFSAs developed by 3M and Solvay, as well as a new multi-acid sidechain perfluoroimide acid ionomer (PFIA) from 3M. Partial neutralization experiments played a key role in systematically manipulating the strength of the electrostatic interactions between proton exchange groups on each sidechain, leading to the elucidation of the molecular-level motions associated with multiple thermal relaxations observed by dynamic mechanical analysis (DMA). Particularly, 3M PFSA and Solvay Aquivion lack an observable β-relaxation in the sulfonic acid-form that is observed in the long sidechain PFSA, Nafion. By varying the strength of the physically-crosslinked network through exchanging the proton on the sulfonic acid groups for large counterions, we were able to conclude that the shorter sidechain length and increase in ion content in the 3M PFSA and Solvay Aquivion serves to restrict the mobility of the polymer backbone such that the onset of segmental motions of the main chains is not observed at temperatures below the α-relaxation temperature, where destabilization of the physically crosslinked network occurs. As a complementary technique to DMA for probing the relaxations in PFSAs, we introduced a new pretreatment method for differential scanning calorimetry (DSC) measurements that uncover a thermal transition in H+-form 3M PFSA, Aquivion, and Nafion membranes. This thermal transition was determined to be of the same molecular origin as the dynamic mechanical α-relaxation temperature in H+-form PFSAs, and the β-relaxation temperature
in tetrabutylammonium (TBA+)-form PFSAs. The thermomechanical relaxations in multi-acid sidechain 3M PFIA were also investigated. Interestingly, the additional acidic site on PFIA led to unexpected differences in thermal and mechanical properties, including the appearance of a distinct glass transition temperature otherwise not seen in PFSA ionomers. We utilized small-angle X-ray scattering (SAXS) studies to probe the differences in aggregate structure between the PFIA and PFSA membranes in order to uncover the morphological origin of the anomalous thermomechanical behavior in PFIA membranes. Larger aggregate structures for PFIA, compared to PFSA, incorporate intervening fluorocarbon chains within the aggregate, resulting in increased spacing between ions that reduce the collective electrostatic interactions between ions such that the onset of chain mobility occurs at lower temperatures than the α-relaxation for PFSA. The SAXS profiles of PFSAs showed two scattering features resulting from scattering between crystalline domains and ionic domains distributed throughout the polymer matrix. In order to fit the "ionomer peak" to models used for the PFIA and PFSA aggregate structure determination, we presented a method of varying the electron density of the ionic domains by using different alkali metal counterions as a tool to make the intercrystalline feature indistinguishable. This allows for isolation of the ionomer peak for better fits to scattering models without any interference from the intercrystalline peak. Lastly, an investigation of annealing PFSAs of different sidechain structures in the tetramethylammonium (TMA+) counterion form above their α-relaxation showed a profound crystalline-like ordering of the TMA+ counterions within the ionic domains. This ordering is maintained after reacidification and leads to improved proton conductivity, which indicates that this method can be used as a simple processing method for obtaining improved morphologies in proton exchange membranes for fuel cell applications.