Sea buckthorn is rich in polyphenolic compounds with antioxidant activities. However, it is very sour, and its odor is slightly unpleasant, so it requires flavor improvement. Fermentation is one potential method. Sea buckthorn juice was fermented at 37 °C for 72 h and then post-fermented at 4 °C for 10 days. The flavor-related properties of the sea buckthorn juice were evaluated during fermentation, including the pH, total soluble solids (TSS), color, sensory evaluation, and volatile flavors. The sea buckthorn fermented juice had a low pH. The total soluble solids decreased from 10.60 ± 0.10% to 5.60 ± 0.12%. The total color change was not more than 20%. Fermentation increased the sweet odor of the sea buckthorn juice, but the fruity flavor decreased and the bitter flavor increased. A total of 33 volatile flavors were identified by headspace gas chromatography–ion mobility spectrometry (GC–IMS), including 24 esters, 4 alcohols, 4 terpenes, and 1 ketone. Their total relative contents were 79.63–81.67%, 10.04–11.76%, 1.56–1.22%, and 0.25–0.55%, respectively. The differences in the characteristic volatile molecular species of the sea buckthorn juice at different fermentation stages could be visually discerned using fingerprint maps. Through principal component analysis (PCA), the total flavor difference of the sea buckthorn juice at different fermentation stages could be effectively distinguished into three groups: the samples fermented for 0 h and 12 h were in one group, the samples fermented for 36 h, 48 h, 60 h, and 72 h were in another group, and the samples fermented for 24 h were in another group. It is suggested that sea buckthorn juice be fermented for 36 h to improve its flavor. GC–IMS and PCA are effective methods of identifying and distinguishing the flavor characteristics of sea buckthorn juice. The above results can provide a theoretical basis for studying the changes in sea buckthorn’s characteristics as a result of fermentation, particularly with regard to its flavor.