In this study, we have designed a three-fluorophore-labeled Y-shaped DNAzyme with a high catalytic cleavage activity and a three-dimensional (3D) MOF-MoS 2 NB (metal−organic framework fused with molybdenum disulfide nanobox), which was synthesized as an efficient quencher of the fluorescent biosensor. The synthesized porous 3D MOF-MoS 2 NBs and Y-shaped DNAzyme exhibited a good analytical response toward the simultaneous multiple detections of Hg 2+ , Ni 2+ , and Ag + ions over the other coexisting metal ions. More specifically, the three kinds of enzyme aptamer and substrate aptamer (SA) were hybridized and annealed to form the Y-shaped DNAzyme structure and labeled with three different fluorophores such as FAM, TAMRA, and ROX over the 3′-end of SA. When the targets were induced, the DNAzyme was triggered to cleave the fluorophore-labeled SAs. Then, the cleaved SAs (FAM-SA, TAMRA-SA, and ROX-SA) were adsorbed on the 3D MOF-MoS 2 NB surface to quench the fluorescence signal due to a noncovalent interaction (van der Waals and π−π stacking interaction), which transmuted the fluorescence on-state to off-state. As a result, the fluorescence assay confiscated the high selectivity and sensitivity for the target analytes of Hg 2+ , Ni 2+ , and Ag + ions achieved for the detection limits of 0.11 nM, 7.8 μM, and 0.25 nM, respectively. Accordingly, the sensitivity of the developed sensor was explored with a better lower detection limit than the previously reported biosensors. The utility of the designed Y-shaped DNAzyme may find a broad field of application in real water sample analysis with interfering contaminants.