In recent years, there has been significant interest in the development of two-dimensional (2D) nanomaterials with unique physicochemical properties for various energy applications. These properties are often derived from the phase structures established through a range of physical and chemical design strategies. A concrete analysis of the phase structures and real reaction mechanisms of 2D energy nanomaterials requires advanced characterization methods that offer valuable information as much as possible. Here, we present a comprehensive review on the phase engineering of typical 2D nanomaterials with the focus of synchrotron radiation characterizations. In particular, the intrinsic defects, atomic doping, intercalation, and heterogeneous interfaces on 2D nanomaterials are introduced, together with their applications in energy-related fields. Among them, synchrotron-based multiple spectroscopic techniques are emphasized to reveal their intrinsic phases and structures. More importantly, various in situ methods are employed to provide deep insights into their structural evolutions under working conditions or reaction processes of 2D energy nanomaterials. Finally, conclusions and research perspectives on the future outlook for the further development of 2D energy nanomaterials and synchrotron radiation light sources and integrated techniques are discussed.