To investigate the chemical differences among different organs (stems, leaves, and fruits) of Acanthopanax senticosus, volatile and non-volatile metabolites were comprehensively characterized for the first time by the combined application of UPLC-Q-TOF-MS and GC-MS. Multivariate statistical analyses, including principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA), were conducted to identify and evaluate differential markers among the three organs. Using variable importance in projection (VIP) > 1 and P < 0.05 as the screening criteria, 47 non-volatile differential metabolites were identified from 177 characterized non-volatile compounds, including 13 flavonoids, 16 phenylpropanoids, 7 triterpenoids, 6 organic acids, 3 amino acids, and 2 other compounds. In addition, 24 volatile differential compounds were screened from 87 identified volatile constituents, comprising 11 olefins, 6 alcohols, 3 ketones, 2 fatty acids, 1 sesquiterpene, and 1 aromatic hydrocarbon. The differential constituents exhibited distinct tissue-specific distribution patterns, with flavonoids predominantly enriched in leaves, phenylpropanoids and lignans enriched in stems, and mono- and sesquiterpenes mainly enriched in fruits. This study systematically elucidated the chemical differences among different organs of Acanthopanax senticosus, providing a scientific basis for its resource development, quality evaluation, and comprehensive utilization.