Alzheimer's disease (AD) is a common neurodegenerative disease that brings great suffering and heavy economic burden to patients. Increasing evidence suggests that peroxynitrite (ONOO−) plays a crucial role in the pathogenesis of AD by mediating neurotoxicity and neuroinflammation. Developing effective peroxynitrite probes to monitor ONOO− is of great significance for the investigation and diagnosis of AD. Herein, two molecular fluorescent probes (NBD-Y and NBD-I) bearing a 7-nitro-2,1,3-benzoxadiazole (NBD) moiety were designed and synthesized for specific ONOO− detection. NBD-Y and NBD-I exhibited a rapid response (within 3 s), low detection limits (11 and 45 nM, respectively), high aqueous solubility (DMSO/PBS = 1: 199, v/v), high selectivity, excellent blood-brain barrier (BBB) penetrability (log P = 3.397), and a ∼78-fold decrease in fluorescence intensity in response to ONOO−. High-resolution mass spectrometry (HRMS), High-performance liquid chromatography (HPLC), and density functional theory (DFT) calculation results indicated that ONOO− may oxidatively break the C-N bond of the probe, resulting in a blue shift of the absorption spectrum due to the principle of intramolecular charge transfer (ICT). Furthermore, NBD-Y has been successfully applied for the detection of endogenous ONOO− in SH-SY5Y cells and is further employed for in vivo imaging in AD mouse models. These results denoted that NBD-Y may serve as a potential biological tool for further understanding the distinct physiological and pathological significance of ONOO−.