Emerging evidence has linked ferroptosis to major chronic diseases such as neurodegenerative and cardio-vascular disorders. Understanding the early stage metabolic network during ferroptosis is essential for uncovering disease mechanisms and developing therapeutic strategies. As oxidative stress occurs in the early phase of ferroptosis, metabolites bearing thiol, amino, and unsaturated carboxyl groups may undergo significant changes. However, their comprehensive profiling remains challenging. Here, we developed a boron beacon−based magnetic chemoselective probe for the targeted enrichment, labeling, and simultaneous mass spectrometric analysis of carboxyl-, amino-, and thiol-containing metabolites in complex biological environments. Compared to conventional probes, our design offers significantly faster reaction kinetics, higher labeling efficiency, and a streamlined workflow. Moreover, the boron-based probes generate distinct isotopic patterns in MS1 and diagnostic fragments in MS2 spectra, enabling precise submetabolome targeting and characterization. Using this strategy, we performed submetabolome profiling of HeLa cells undergoing ferroptosis and identified 303 dysregulated metabolites. The results revealed coordinated perturbations in key metabolic pathways, including transsulfuration, fatty acid biosynthesis, and glutathione metabolism. This work not only provides mechanistic insights into ferroptosis regulation but also establishes a high-throughput and functionally guided platform for metabolomic network analysis for future studies.（DOI：10.1021/acs.analchem.5c05834）