A distribution of Cu ions in polyelectrolyte film (Nafion) is directly observed with a small-angle X-ray scattering (SAXS) method utilizing an X-ray anomalous dispersion effect. A partial structure factor of the Cu ions, GAA(q), can be derived from the SAXS profiles obtained by scanning the incident X-ray energy around the Cu K absorption edge. GAA(q) has two peaks, indicating that the Cu ions hierarchically distribute in Nafion film. In addition, a standard SAXS also shows that Nafion film has a hierarchical structure. These results mean that the Cu ions locate in the domain where the hydrophilic bases aggregate.