The rapid diffusion kinetics and smallest ion radius make protons the ideal cations toward the ultimate energy storage technology combining the ultrafast charging capabilities of supercapacitors and the high energy densities of batteries. Despite the concept existing for centuries, the lack of satisfactory electrode materials hinders its practical development. Recently, the rapid advancement of the emerging two-dimensional (2D) materials, characterized by their ultrathin morphology, interlayer van der Waals gaps, and distinctive electrochemical properties, injects promises into future proton-based energy storage systems. In this perspective, we comprehensively summarize the current advances in proton-based energy storage based on 2D materials. We begin by providing an overview of proton-based energy storage systems, including proton batteries, pseudocapacitors and electrical double layer capacitors. We then elucidate the fundamental knowledge about proton transport characteristics, including in electrolytes, at electrolyte/electrode interfaces, and within electrode materials, particularly in 2D material systems. We comprehensively summarize specific cases of 2D materials as proton electrodes, detailing their design concepts, proton transport mechanism and electrochemical performance. Finally, we provide insights into the prospects of proton-based energy storage systems, emphasizing the importance of rational design of 2D electrode materials and matching electrolyte systems.