Two-dimensional MXene materials perform excellently in supercapacitor applications, but self-stacking and overlap limit their applications. Constructing a reasonable layered structure by combining MXene and graphene can effectively inhibit the restacking and overlap of MXene and improve the performance of supercapacitors. In this work, we studied the energy storage performance of a conventional MXene electrode and MXene/graphene composite electrode in sulfuric acid aqueous electrolyte by molecular dynamics (MD) simulation and analyzed their energy storage mechanisms. The simulation results reveal that the MXene/graphene composite electrode showed faster charge-discharge speed and larger capacity and had more obvious advantages as a cathode. The charging process of the composite cathode can be divided into two stages. In the first stage, SO42- and H3O+ enter the electrode as a whole in a nearly 1:2 ratio, and a unique three-layer structure is formed in the graphene area, while a large number of HSO4- leaves the electrode. In the second stage, SO42- with a part of H3O+ (ratio of 2:2 to 2:3) leave the electrode, and the three-layer structure is gradually destroyed. The cooperation of these two stages leads to a particular "concave" in the total energy change of the composite cathode. The introduction of graphene has brought about changes in ion distribution, migration mechanism, and energy change, making the MXene/graphene cathode show significant advantages in energy storage. This work is of great significance for understanding the microscopic energy storage mechanism of MXene/graphene-based electrodes.