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The volatile components in Houttuynia cordata Thunb. have a distinctive odor, which is the source of their unique flavor as food. Although volatile compounds are widely present in Houttuynia cordata Thunb., little is known about their accumulation in vertical distribution in different organs. In this study, gas chromatography-mass spectrometry (GC-MS) and chemometrics were used to determine volatile substance's types and relative contents, especially 2-undecanone in different parts of Houttuynia cordata Thunb. The results showed that 933 species and 16 classes of volatile compounds were identified in the leaves, aerial stems, subterranean stems, and roots. Among them, the accumulation of 2-undecanone, d -limonene, and α-pinene were significantly higher in subterranean stems than in other organs. The related KEGG pathway-limonene and pinene degradation, was identified. The study's results can provide a reference for the industrial extraction and utilization of volatile compounds from different parts of Houttuynia cordata Thunb. • The first analyze to volatile compounds in four different organs of H. cordata. • 933 species volatile compounds were identified. • 2-undecanone was significantly accumulated in subterranean stems. • The KEGG pathway cluster analysis provided reference for regulation mechanism. • Reveal the reasons why people in different regions like to eat different parts. [ABSTRACT FROM AUTHOR]