Abstract: In this study, the precious tree species Dalbergia odorifera was investigated using Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-Q-TOF-MS) to systematically analyze the distribution characteristics of 4 key secondary metabolites—Sativanone, Vestitone, (-)-Medicarpin, and Formononetin—across 6 radial zones of the xylem: Outer Sapwood (OSW), Middle Sapwood (MSW), Inner Sapwood (ISW), Outer Transition Zone (OTZ), Inner Transition Zone (ITZ), and Heartwood (HW). The results demonstrated a significant increasing trend in the content of all four secondary metabolites from the outer sapwood to the heartwood, indicating that heartwood formation is accompanied by continuous synthesis and accumulation of these compounds. Furthermore, Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) was employed to resolve the spatial distribution patterns of flavonoid metabolites within xylem tissues. These characteristic metabolites are predominantly enriched in the heartwood region, with a non-uniform distribution pattern. Signal intensity in heartwood fiber tissues was significantly stronger than that in parenchyma tissues.