In this study, a dual-mode biosensor based on the heterojunction of Cu2O@Cu2S/D-TA COF was constructed for ultra-sensitive detection of Hg2+ using both photoelectrochemical and electrochemical approaches. Briefly, a 2D ultra-thin covalent organic framework film (D-TA COF film) with excellent photoelectrochemical signals was prepared on ITO surfaces through an in situ growth method. Subsequently, the probe H1 was immobilized onto the biosensor via Au–S bonds. In the presence of Hg2+, the formation of T-Hg2+-T complexes triggered hybridization chain reactions (HCR), leading to the attachment of abundant Cu2O@Cu2S probes onto the biosensor. As a p-type semiconductor, Cu2O@Cu2S could form a heterojunction with the underlying D-TA COF films. Meanwhile, it exhibited catalase-like activity, and the O2 produced by its catalytic decomposition of H2O2 can interact with the D-TA COF films, thus achieving double amplification of the photocurrent signal. Benefiting from the excellent and inherent Cu2+/Cu+ redox pairs of Cu2O@Cu2S, satisfactory differential pulse voltammetry (DPV) signals were obtained. As expected, the dual-mode biosensor was realized with wider linear ranges and low detection limits. Additionally, the analytical performance for Hg2+ in real water samples was excellent. Briefly, this suggested approach offers a facile and highly efficient modality for monitoring heavy metal ions in aquatic environments.