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Abstract CuxO with flower‐like hierarchical structures has attracted significant research interest due to its intriguing morphologies and unique properties. The conventional methods for synthesizing such complex structures are costly and require rigorous experimental conditions. Recently, the X‐ray irradiation has emerged as a promising method for the rapid fabrication of precisely controlled CuxO shapes in large areas under environmentally friendly conditions. Nevertheless, the morphological regulation of the X‐ray‐induced synthesis of the CuxO is a multi‐parameter optimization task. Therefore, it is essential to quantitatively reveal the interplay between these parameters and the resulting morphology. In this work, we employed a high‐throughput experimental data‐driven approach to investigate the kinetics of X‐ray‐induced reactions and the impact of key factors, including sputtering power, film thickness, and annealing of precursor Cu thin films on the morphologies of CuxO. For the first time, the flower‐like CuxO nanostructures were synthesized using X‐ray radiation at ambient condition. This research proposes an eco‐friendly and cost‐effective strategy for producing CuxO with customizable morphologies. Furthermore, it enhances comprehension of the underlying mechanisms of X‐ray‐induced morphological modification, which is essential for optimizing the synthesis process and expanding the potential applications of flower‐like structures.