Tree peonies (Paeonia suffruticosa) are important pharmaceutical and oilseed crops widely cultivated in China. Tree peony flowers, as important by-products of the industrial crops, are conventionally used as folk medicine with health-promoting effects on human. However, the in-depth understanding of biologically active compounds in tree peony flowers is scarce. In this study, an in-depth analysis of bioactive compounds in tree peony flower buds (TPFBs) from 74 cultivars was conducted using an integrated LC-MS-based metabolomic approach. Ninety-two metabolites were tentatively identified in TPFBs. The quantitative results revealed that TPFBs were abundant in bioactive compounds. Among these, paeoniflorin, albiflorin, cynaroside, and pentagalloylglucose (PGG) emerged as the primary chemical markers of TPFBs, showing significant variations based on genotype. Each extract of TPFB exhibited potent antioxidant, antibacterial, and anti-neuroinflammatory activities. Notably, TPFB extract showed the highest effectiveness in inhibiting L. monocytogenes among all tested bacteria. Cynaroside was predicted to serve as a pivotal component in TPFB for its anti-neuroinflammatory effects by interacting with toll-like receptor 4 (TRL4) and interleukin-1beta (IL-1β). This study offers novel insights into the bioactive compounds and bioactivities of TPFBs, which lays theoretical basis for the application in pharmaceutical industry.