Three different morphology controlled copper oxide materials (porous microspheres, flower-like, and thorn-like CuO) were prepared by facile and environmentally friendly processes, which were further investigated for their electrochemical properties and performance at lithium-ion battery anodes. CuO microspheres were prepared by simply solution chemistry, whereas flower-like and thorn-like CuO structures were prepared hydrothermally, with the structural transformations arising due to selection of chloride or sulfate counter ions in the precursor salts, respectively. After a 400°C heat treatment in air, the morphology controlled materials demonstrated excellent phase purity as indicated by X-ray diffraction (XRD), and we propose a growth mechanism for the various materials based on systematic investigation of the structure and properties of the intermediate species. The electrochemical and lithium-ion battery performance employing the shape controlled CuO materials was investigated, allowing for elucidation of the synthesis–structure–performance correlations of CuO-based anodes. The performance of lithium-ion batteries was found to be highly dependent on the CuO morphology. The CuO microspheres exhibit a superior electrochemical performance to the other two CuO samples in terms of cycle capacity and rate performance, indicating a viable strategy to prepare next-generation lithium-ion battery systems with improved storage capacities.