Two through‐bond energy transfer fluorescent probes with a dihydroxyl naphthyl‐pyrenyl conjugated system were synthesized for long‐acting cyclic monitoring and eliminating peroxynitrite (ONOO−). The probes exhibit large Stokes shifts (230 or 280 nm) and the fluorescence at 620 or 652 nm rapidly change in response to continuously variable concentrations of ONOO− under physiological conditions. The probes show good reversibility and can rapidly monitor the concentration changes of ONOO− in real time. In addition, with the additions of the probes, the decomposition of ONOO− is greatly accelerated. Therefore, the probes can effectively eliminate the excess ONOO− as well as sensing it. The biological studies showed that the probes can effectively and reversibly eliminate both exogenous and endogenous ONOO− in‐situ as well as sensing its changes in cells, which can help to maintain the normal physiological concentration of ONOO− in organisms. This is the first system that a probe achieves multifunction including real‐time detection, long‐acting cyclic monitoring and in‐situ elimination, thereby maintaining a normal physiological balance for ONOO−.