As a bioactive species with high oxidation capacity, peroxynitrite (ONOO-) plays a crucial role in the regulation of diverse pathophysiological processes, and the overproduction of ONOO- is closely associated with various physiological diseases such as liver injury, pulmonary fibrosis and so on. Herein, two borate-based fluorescent probes 3a and 3b were synthesized for monitoring ONOO- by a simple substitution reaction. The experimental results showed that 3a and 3b had high selectivity and sensitivity for ONOO-. The detection limits of 3a and 3b were 79.46 nM and 32.12 nM, respectively. Moreover, the recognition was not disturbed by other active oxygen groups and common ions. More importantly, the probes 3a and 3b had low cytotoxicity and were successfully used to detect endogenous and exogenous ONOO-. They would provide an efficient detection method for further exploring the physiological and pathological role of ONOO- in complex biological systems and related diseases.