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The purpose of this study was to explore the volatile characteristic flavor compounds in sea-buckthorn yoghurt, and to clarify the influences of fermentation with sea-buckthorn on the quality and flavor compounds of yoghurt. The volatile compounds were analyzed by sensory evaluation and headspace solid phase microextraction gas chromatography ion mobility spectrometry (HS-SPME-GC-IMS) combined with multivariate statistical analysis method to realize the characterization of characteristic volatile compounds in fermented sea-buckthorn yoghurt. The results showed that sea-buckthorn yoghurt had many volatile substances, and the main sources of volatile substances were esters, ketones and aldehydes. The fermentation process reduced the sour taste of sea-buckthorn juice, made the taste softer and the aroma richer and more typical. The principal component analysis (PCA) was used to screen out compounds that contributed more to aroma, and the cluster heat map analysis was used to classify volatile compounds into three categories. Among them, 2,2,4,6,6-pentamethylheptane, ethyl acetate(monomer), ethyl 2-methylbutanoate, propyl butanoate, butyl formate(dimer), 2-furfurylthiol,formic acid, 3-methylbutyl ester, ethyl acetate(dimer) and butyl formate(monomer) were the main flavor substances of fermented sea-buckthorn yoghurt. This study provided a research idea for the characteristic flavor of compound yogurt, and the results provided a theoretical basis for the subsequent flavor improvement of sea-buckthorn yogurt.