Aqueous batteries and supercapacitors are promising electrochemical energy storage systems (EESSs) due to their low cost, environmental friendliness, and high safety. However, aqueous EESS development faces challenges like narrow electrochemical windows, irreversible dendrite growth, corrosion, and low energy density. Recently, two-dimensional (2D) transition metal carbide and nitride (MXene) have attracted more attention due to their excellent physicochemical properties and potential applications in aqueous EESSs. Understanding the atomic-level working mechanism of MXene in energy storage through theoretical calculations is necessary to advance aqueous EESS development. This review comprehensively summarizes the theoretical insights into MXene in aqueous batteries and supercapacitors. First, the basic properties of MXene, including structural composition, experimental and theoretical synthesis, and advantages in EESSs are introduced. Then, the energy storage mechanism of MXene in aqueous batteries and supercapacitors is summarized from a theoretical calculation perspective. Additionally, the theoretical insights into the side reactions and stability issues of MXene in aqueous EESSs are emphasized. Finally, the prospects of designing MXene for aqueous EESSs through computational methods are given.