The microstructural properties of polycrystalline CuO powders and their evolution during controlled high energetic ball milling (HEBM) were studied using conventional X-ray diffraction (XRD) techniques and in situ temperature-dependent small and wide angle scattering (SAXS-WAXS) synchrotron radiation experiments. Volume weighted average grain size, unit cell expansion, oxygen deficiency, and microstrain values as a function of milling time were obtained from XRD. SAXS data revealed different nanostructures for samples synthesized by one-step solid-state reaction (SSR) or HEBM-treated powders. The latter presented the characteristics of a multilayered nanoscale solid system with surface fractal behavior. Correlation of the XRD microstructural parameters and the power law exponent of the SAXS curves as a function of temperature and milling time provided a coherent picture of the structure of HEBM-treated powders. The overall structural information presented in this article may shed some light on the macroscopic physical properties of CuO nanostructures.