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Introduction Poria cocos , a fungus recognized for both its edible and medicinal properties, is highly valued for its bioactive effects, such as immune modulation, improvement of digestive function, inflammation reduction, and enhancement of sleep quality. Typically, three parts of Poria cocos --Poria, Poriae cutis, and Poria cum radice pini --are utilized in functional foods. Methods This research applied Gas Chromatography -Ion Mobility Spectrometry (GC-IMS) alongside chemometric techniques to compare the volatile organic compounds (VOCs) present in these three sections. Analytical methods including Principal Component Analysis (PCA), Cluster Analysis (CA), Euclidean Distance Analysis, and Partial Least-Squares Discriminant Analysis (PLS-DA) were used. Results The study identified 104 VOCs, predominantly aldehydes, ketones, alcohols, and terpenoids. Among them, PC-01 and PC-03 contain two compounds that PC-02 lacks, and PC-02 and PC-03 contain ten compounds that PC-01 lacks. Furthermore, 3-octanone and 4-methyl-3-penten-2-one are unique to PC-02, while β-Ocimene, 1,8-cineole, 2-methyl-2-pentenal, and Sabine are unique to PC-03. The findings lay the groundwork for the precise application of specific parts of Poria cocos in dietary and medicinal contexts. Conclusion In particular, the study helps to clarify the biochemical factors contributing to the anxiolytic effects of Poria cum radice pini, such as L-Perillaldehyde, which is a neuroactive compound, and linalool, which is recognized for its anti-anxiety, anti-tumor, sedative, and hypnotic properties. This study thereby supports targeted innovations in the development of health products from various parts of Poria cocos .