In situ X-ray diffraction (XRD), as a widely used tool in probing the structure evolution in electrochemical process as well as the energy storage and capacity fading mechanism, has shown great effects with optimizing and building better batteries. Based on the research progresses of in situ XRD in recent years, we give a review of the development and the utilization of this powerful tool in understanding the complex electrochemical mechanisms. The studies on in situ XRD are divided into three sections based on the reaction mechanisms: alloying, conversion, and intercalation reactions in lithium-ion batteries. The alloying reaction, in which lithium ions insert into Si, Sb, and Ge is firstly reviewed, followed by a discussion about the recent development of in situ XRD on conversion reaction materials (including metal oxides and metal sulfides) and intercalation reaction materials (including cathode materials and some structure-stable anode materials). As for sodium-ion batteries, we divide these researches on structure evolution into two categories: cathode and anode materials. Finally, the future development of in situ XRD is discussed.