The inappropriate and excessive utilization of antibiotics in medicine, agriculture, and the environment significantly threatens human health and ecosystems. Consequently, developing on-site and sensitive methods for the detection of antibiotics is urgently needed. In this study, we presented a novel fluorescence/colorimetric/smartphone triple-mode sensor for highly sensitive and intuitive detection of enrofloxacin (ENR). The ENR-specific aptamers (Apt) modified with gold nanoclusters (Au NCs) were loaded onto the magnetic covalent organic frameworks (Fe3O4@COF NPs). The resulting Fe3O4@COF-Apt-Au NCs sensor exhibited aptamer-regulated nanozyme activity and fluorescence changes. Within this sensor, the fluorescence of Au NCs was significantly diminished, and the peroxidase-like activity of the Fe3O4@COF NPs was markedly inhibited due to the masking of active sites. Upon exposure to ENR, the specific interaction between the aptamers and ENR prompted the dissociation of Apt-Au NCs from the carrier surface. This dissociation facilitated the recovery of fluorescence signals from Au NCs for fluorescence analysis and enhanced the peroxidase-like activity of Fe3O4@COF NPs for colorimetric analysis. Meanwhile, the expanded use of smartphones facilitates the development of a real-time, portable method for ENR assay. The proposed triple-mode platform exhibited strong linearity for ENR concentrations of 0.01–1 × 104 ng/mL (fluorescence), 10–5 × 104 ng/mL (colorimetry and smartphone), with detection limits of 4.65 × 10−3, 0.07 and 0.12 ng/mL, respectively. Furthermore, the sensor demonstrated potential for effective detection of ENR in real samples. The mutual verification provided by the sensor enhances the reliability and accuracy of ENR detection in both environmental and animal-derived food samples.