Inflammation, a central process in numerous diseases, plays a crucial role in hepatic disorders, arthritis, cardiac conditions, and neurodegenerative ailments. Given the lack of effective anti-inflammatory drugs, it is imperative to assess inflammation severity and explore novel therapeutics. Selenocysteine (Sec), a key mediator of selenium's biological function, is closely involved in anti-inflammatory responses. We have synthesized a novel near-infrared fluorescent probe, Sec-BDP, which can image Sec dynamics in vivo with high selectivity and sensitivity. Sec-BDP detects Sec at concentrations as low as 0.085 μM. Utilizing this probe, we visualized Sec levels in cell, zebrafish, and mouse inflammation models, enabling a clear assessment of inflammation severity. To screen for drug candidates, Sec-BDP was integrated with ultrahigh performance liquid chromatography quadrupole time-of-flight mass spectrometry to identify potent anti-inflammatory compounds in Astragalus membranaceus, such as 5-O-methylvisammioside. Imaging of Sec with Sec-BDP provides insights into Sec-related diseases and aids in discovering new treatments. This probe advances selenium biology and promises more targeted therapeutic strategies.