Real-time monitoring of adenosine-5′-triphosphate (ATP) and investigating its ability to bind Fe 3+ are of great significance for tracking of Fe 3+ in cells and cell functions. However, most nanomaterials for fluorescent nanoprobes have been randomly designed, and there are no reports about band gap of nanomaterials for matching with the redox potential of Fe 3+ / Fe 2+ , which could be helpful for further sequential sensing of Fe 3+ and ATP in cells. Herein, the fluorescent nanoscale covalent organic framework (NCOF) is synthesized and has −2.97 eV of the conduction band and 0.87 eV of the valence band from the theoretical calculations. Coincidentally, the energy band of NCOF fluorescence excellently meets the requirements of energy transfer for the redox potential of Fe 3+ /Fe 2+ (0.77 V vs normal hydrogen electrode (NHE)). This allows us to easily design a NCOF-based fluorescent probe for sensing Fe 3+ and ATP in cells. The experimental results demonstrated that the NCOF biosensor had significant superiority in Fe 3+ and ATP detection, which had a broad linear response to Fe 3+ and ATP, ranging from 0.5 to 100 μM and 0.005 to 5 μM, respectively. These results allowed to achieve ultralow detection limits of 0.061 and 0.0024 μM for the detection of Fe 3+ and ATP in cells, respectively. Based on the excellent fluorescence properties and good biocompatibility of the NCOF, the probe has been further used for sensitive imaging of Fe 3+ and real-time dynamic monitoring of ATP in cells. In addition, the mechanism of interaction among NCOFs, Fe 3+ , and ATP was first verified by theoretical calculations. These results are promising to improve the development of fluorescent nanoprobes for biosensor and bioimaging applications.