In recent years, aqueous rechargeable lithium-ion batteries (ARLIBs) have attracted attention as an alternative technology for electrical storage. One of the perspective battery anode materials for application in ARLIBs is Bi2Se3, which has already shown good perspectives in the application of conventional lithium-ion batteries (LIBs) that use organic electrolytes. In this study, the electrochemical properties of Bi2Se3 thin films with two different layers on the electrode surface—the solid electrolyte interphase (SEI) and the Bi2O3 layer—were investigated. The results of this work show that the formation of the SEI layer on the surface of Bi2Se3 thin films ensures high diffusivity of Li+, high electrochemical stability, and high capacity up to 100 cycles, demonstrating the perspectives of Bi2Se3 as anode material for ARLIBs.