An original analysis of the structure of ionomer films along the three dimensions using micro small-angle X-ray scattering (microSAXS) technique is reported. While the in-plane structure appeared as isotropic, a significant SAXS anisotropy was observed in the transverse direction, revealing a multiscale structural anisotropy from the molecular level to several tens of nanometers. Using transmission and scanning electron microscopy (TEM and SEM, respectively), a layered structure was identified up to micrometer scales. This structural anisotropy was used to interpret the conductivity data as a function of the ion content. Moreover, the diffusion coefficients of the counterions, were determined along the planar and transverse directions using pulse field gradient spin echo-NMR (PFGSE-NMR) in order to correlate structure and transport properties.