RationaleThe volatile organic compounds (VOCs) of Alpinia katsumadai Hayata (AKH) play a key role in determining its effects such as organoleptic properties, medicinal properties, and consumer preferences. The nonmedicinal parts (roots, fibrous roots, stems, leaves, and shells) in AKH are also rich in VOCs and different degrees of antibacterial activity. Therefore, it is important to comprehensively characterize the VOCs in different parts of AKH and learn about their potential antimicrobial abilities.MethodsIn this study, headspace gas chromatography‐ion mobility spectrometry (HS‐GC‐IMS) and headspace solid‐phase microextraction gas chromatography–mass spectrometry (HS‐SPME‐GC‐MS) were used to comprehensively investigate the compositional characteristics and differences of roots, fibrous roots, stems, leaves, shells, and seeds in AKH. Multivariate statistical analysis was used to determine the differential VOCs in different parts of AKH. The inhibition zone diameter method was used to compare the antibacterial ability of different parts.ResultsHS‐GC‐IMS and HS‐SPME‐GC‐MS analyses identified 67 and 125 VOCs, respectively. Multivariate statistical analysis showed the differences in the six parts is obvious. Compounds such as (E)‐2‐heptenal and thymol were selected as potential VOCs to distinguish six sites of AKH. In general, the inhibition effect of the volatile oils from shell and root on the two colonies was better, and the volatile oils of the four parts of AKH have better inhibitory effect on Staphylococcus aureus.ConclusionThis research conducted a comprehensive analysis of the fundamental volatile components in AKH. It subsequently elucidated the distinctions and specificities in different parts. The antibacterial effect of volatile oil in different parts was further compared, which was conducive to finding alternative parts for seeds in some active aspects, and the utilization of AKH was more sufficient.