Ion-containing polymers are of intense interest for applications in energy storage and conversion devices. The conductivities of these polymers are determined by both the ion mobility and the total number of mobile charge carriers, which in turn depend on the chemical structure and morphology. To rationally design ion-containing polymers with high conductivity, a comprehensive understanding of their multi-scale structure is essential. The morphologies of several ion-containing polymers have been explored as a function of material chemistry and external stimuli by X-ray scattering, scanning transmission electron microscopy, and various types of spectroscopy. The fundamental structure-property relationships in ion-containing polymers are discussed. Two classes of ion-containing polymers with very different aggregation behaviors have been studied. The first class is the polystyrene-based ionomers, where there are unfavorable interactions between the polymer matrix and ionic groups. The ionic functional groups in these hydrocarbon-based ionomers self-assemble into ionic aggregates, due to the strong electrostatic interactions in the low dielectric constant matrix and the lack of any solvation interactions between ions and hydrocarbons. The effects of acid content, neutralization level, and cation type on the size, number density, and composition of ionic aggregates were explored. The morphological findings provide a framework for interpreting the dielectric relaxation behaviors of the same ionomers, so as to establish correlations between structure and dynamics. The second class is poly(alkyl oxide)-based ionomers. The ionic groups have favorable interactions with the polymer matrix in poly(ethylene oxide) (PEO)-based polyester ionomers or urethane groups in poly(tetramethylene oxide)-based polyurethane ionomers. The states of ions are highly dependent on the PEO length, cation size and temperature in PEO-based ionomers. Decreasing cation size from Cs to Li results in a transition of ionic states from isolated ion pairs to aggregated ion pairs. As the temperature increases, these ionomers exhibit greater microphase separation of the ionic groups due to the decreased ability of PEO to solvate the ions. These findings combine to greatly advance our understanding of the interplay between morphology and ion conduction in single-ion conductors.