Marine biotoxins poison seafood under conditions of eutrophication induced by harmful algal blooms, threatening life. It is challenging to construct efficient sensing technologies for trace marine biotoxins. Herein, we utilized Fe(III) and Zr(IV) to prepare bimetal-organic frameworks (ZrFe-MOF). The synergism between the two metals endowed ZrFe-MOF with high peroxidase-like activity, excellent stability, and good dispersity in aqua. Our results demonstrated that the inherent peroxidase-like activity of ZrFe-MOF was inhibited by the aptamers absorbed on this material surface. The effect mechanism was unraveled by clarifying the structural and electronic interactions. Meanwhile, the preferential binding between these specific aptamers and cognate targets triggered the release of rigid complexes from the surface of ZrFe-MOF, resulting in the reactivation of the peroxidase-like activity. Based on the reversible inhibition–activation nanozyme activity controlled by aptamers, a facile ZrFe–MOF-based colorimetric assay was proposed for the detection of marine biotoxins. This strategy was used to determine tetrodotoxin (TTX) as a proof of concept. The limit of detection (LOD) was as low as 0.07 ng/mL, and the detection range was 0.1–200 ng/mL. Furthermore, this assay could be used to successfully analyze natural TTX-contaminated puffer fish and clam samples. Efficient analytical performance was achieved. Notably, the discrimination of multiple marine biotoxins was successfully achieved in seawater based on the pattern recognition process. This study offers a paradigm for tuning MOF nanozyme activity in the presence of nucleic acids. The results bring new insights for developing multi-sensing platforms for various applications.