Aqueous energy storage technologies, including aqueous supercapacitors and aqueous batteries, have attracted extensive research interest owing to their great potential for diverse applications. Water-based electrolytes enable aqueous energy storage devices with advantageous features, such as fast charging capability, high power density, eco-friendliness, low cost, and large-scale manufacturing. The development of advanced electrode materials is highly pursued to improve the performance of aqueous energy storage devices. In this regard, van der Waals (vdW) layered transition metal-containing compounds (LTMCs) have been brought into the spotlight due to their high theoretical specific capacity and versatile possibilities for structure engineering. This review highlights the recently developed structure engineering strategies for LTMCs in the applications of aqueous energy storage. Particular efforts are made to emphasize the correlation between the engineered vdW structure of LTMCs and their energy storage behaviours. Lastly, we provide an outlook about the future challenges in this field, which will hopefully inspire more exploration on LTMC-based aqueous energy storage devices.