Spuriopimpinella brachycarpa (2n = 2x = 22), a perennial Apiaceae herb traditionally consumed in Northeast China, is rich in bioactive compounds such as flavonoids and terpenoids and possesses both medicinal and comestible value. However, the metabolic mechanisms underlying these traits remain unclear due to the lack of genomic resources. Here, we present the first chromosome-level genome assembly of S. brachycarpa (4.12 Gb; scaffold N50 = 358.95 Mb; 11 chromosomes). Comparative genomics analysis revealed two postdivergence whole-genome duplication (WGD) events in Apiaceae and a close phylogenetic relationship between S. brachycarpa and Daucus carota (carrot). Metabolomic profiling indicated that flavonoids, dominated by flavanols and flavones, are most actively synthesized in leaves, with their biosynthesis likely regulated by the MYB transcription factor SbraChr11G00348720.1. Terpenoids, primarily monoterpenes and sesquiterpenes, accumulated predominantly under cultivated conditions, demonstrating habitat-specific patterns. Transcriptomic analysis further identified two key terpene synthase genes—SbraChr6G00204720.1 (TPS-a subfamily) and SbraChr3G00078100.1 (TPS-b subfamily)—associated with sesquiterpene and monoterpene biosynthesis, respectively. By integrative genomic, transcriptomic, and metabolomic data, this study systematically elucidates the biosynthesis basis of major secondary metabolites in S. brachycarpa and provides a valuable genetic resource for comparative genomics and molecular breeding in Apiaceae crops.

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