Abstract: Sea bucthorn (Hippophae rhamnoides) fruits are gradually used to develop various functional foods, due to their high edible and medicinal values rich in nearly 200 kinds of nutrients and active substances, such as polyphenols, polysaccharides, carotenoids, and flavonoids. This present research aims to clarify the difference of Sea bucthorn from the representative places of origin, in order to provide the selection basis for the research and development of the Sea bucthron nutritious products. The Sea bucthorn was collected from Shanxi, Hebei, Inner Mongolia, and Xinjiang in China. The varieties of Sea buckthorn were mostly used in the processing (Hippophae rhamnoides. L. Zhongguoshaji, Hippophae rhamnoides. L. Yulushaji, Hippophae rhamnoides. L. Neimenggushaji, and Hippophae rhamnoides. L. Altaydaguoshaji). The quality of fruit was comprehensively evaluated from the aspects of color, texture, taste, flavor, and nutritional components. Gas Chromatography-Mass Spectrometry (GC-MS) and Ultra-High Performance Liquid Time-Of-Flight Mass Spectrometry (UHPLC-QTOF-MS) were selected to determine the volatile components and small molecule active substances. The comprehensive quality of Sea buckthorn was explored to determine the difference in four regions of China. The results showed that the Sea bucthorn from Xinjiang was the brightest among the four regions. The highest sugar-acid ratio (1.997) was found in the Sea bucthorn from Inner Mongolia. The sea bucthorn from Hebei Province presented the highest polyphenol content (1.14 mg/g). By contrast, Xinjiang Sea buckthorn shared the highest carotenoid content (37.15 mg/100 g). However, there was no significant difference (P>0.05) in the vitamin C content of the sea buckthorn from four regions (21-23 mg/100 g). Moreover, there was a significant difference (P<0.05) in the antioxidant activity of sea bucthorn from the four regions. In addition, the Shanxi Sea bucthorn possessed the highest scavenging rate of DPPH free radical. Inner Mongolia sea buckthorn presented the highest ABTS free radical scavenging rate and iron ion reduction ability (FRAP).A total of 153 compounds were detected in the sea buckthorn from the four regions, indicating the significant difference in the volatile components. The characteristic volatile substances in the Hebei sea buckthorn were 3-octanone, 2-heptenal, and amyl isobutyrate, whereas, there were the isopropyl isovalerate, propyl 2-methylbutyrate, and (methylthiol) ethyl acetate in Inner Mongolia. The n-octane,2, 3-dihydro2,2, 6-trimethylbenzalde hyde was found in the XinJiang sea buckthorn, whereas, the amyl hexanoate, basil, and ethyl decanoate were in the Shanxi one. 61 compounds were detected in the small molecular active components, among which the main polyphenols were quinic acid, isorhamnetin, aloxone sugar, kaempferol, and quercetin. On the whole, the Inner Mongolia sea buckthorn was the strongest antioxidant capacity and the highest sugar-acid ratio, indicating a promising potential raw material for functional products and health products. The characteristic components of sea buckthorn from the Shanxi were 1, 3-dihydroxy-12, 24-dienoic acid, quinic acid, and 2- (2-ethyl butyryl) amino-4, 5-dimethoxybenzoic acid. The characteristic components of sea buckthorn from Xinjiang were mainly 1-oleyl-glycerol-3-phosphocholine, and aloxone. A comprehensive comparison was performed on the physicochemical characteristic of representative sea bucthoron in the XinJiang, Inner Mongolia, Shanxi, and Heibei regions. A factor analysis was carried out on the 14 quality indexes of Sea buckthorn. Among them, three common factors were extracted, where the cumulative variance contribution rate reached 100%. The contribution rate of the first common factor reached 45.831%, followed by 38.623%, and 15.546%. The comprehensive quality scores of the representative sea buckthorn varieties were ranked in descending order of the Hebei, Shanxi, Inner Mongolia, and Xinjiang sea buckthorn, according to the comprehensive quality evaluation model. A better performance was achieved to compare the color, taste, flavor, active component, and antioxidant quality of sea buckthorn in four regions of China. The finding can provide the technical reference and application approaches for the raw material selection in the series of sea buckthorn products.