Abstract: In order to investigate the changes in fatty acid compounds and volatile compounds during the processing of sea buckthorn whole fruit powder, this study used sea buckthorn as the research object and employed targeted metabolomics combined with gas chromatography-ion mobility spectrometry (GC-IMS) technology, along with principal component analysis (PCA), correlation analysis (CorrA) and other chemometric methods to preliminarily investigate the dynamic changes and correlations of fatty acids and volatile components during the processing of sea buckthorn whole fruit powder. The results showed that 34 fatty acid compounds in sea buckthorn whole fruit powder were identified from sea buckthorn whole fruit powder by ultra-performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-QQQ-MS), among which Linoleic acid (0.48~10.78 ng/mg) and palmitoleic acid (0.03~5.91 ng/mg) were the main fatty acid compounds. The total fatty acid content (2.48~114.84 ng/mg) in sea buckthorn whole fruit powder showed an overall decreasing trend during processing, with particularly significant decreases during the pulping and drying stages (P<0.05). These decreases represent reductions of 40.67% and 62.6%, respectively, compared to the raw material thawing stage. A total of 41 volatile compounds were identified by GC-IMS, showing an overall trend of first decreasing and then increasing. Based on VIP values>1, 12 key volatile compounds were screened, including hexanal, aromatic alcohols, and butyl 2-methylbutyrate. Combined with ROVA analysis, hexanal was identified as the primary characteristic volatile compound. Correlation analysis revealed that oxidized linalool was positively correlated with all fatty acid compounds. Further KEGG pathway analysis of the production pathways of major volatile compounds clarified that degraded lipids are primarily enriched in the fatty acid metabolism pathway, and fatty acid compounds derived from the unsaturated fatty acid biosynthesis pathway contribute to the formation of characteristic volatile flavor compounds such as hexanal, 2-pentanone, and 2-hexanone in sea buckthorn whole fruit powder. This study lays the foundation for improving the quality of sea buckthorn whole fruit powder.