Abstract: Seabuckthorn fruit is one of the most nutritious and medicinal berries. This study aims to analyze the fruit quality and medicinal components in the Xinjiang seabuckthorn under spatial distribution differences. The test bases were taken as the seabuckthorn plantations in five counties of the main seabuckthorn resource distribution areas in Xinjiang (Qinghe county in Altay Prefecture, Buerjin county in Altay Prefecture, Habahe county in Altay Prefecture, Wushi county in Aksu Prefecture, and Aheqi county in Kizilsu Kirgiz Autonomous Prefecture). Three seabuckthorn varieties of 'Shenqiuhong', 'Wucifeng' and 'Zhuangyuanhuang' were used as test samples. Some indicators of mature seabuckthorn fruits were determined, such as the basic factors, trace elements, functional quality, and medicinal components. Data support was also provided to optimize the planting structure of seabuckthorn resources, in order to promote the modernization, large scale and standardization in industrial production. Specifically, the sampling was carried out on the plantations in the distribution area of seabuckthorn. Three planting plots were selected for each variety, i.e., nine planting plots were from each county (only three planting plots were selected in Wushi county, because only distributed 'late autumn red'). The 'five-point' was captured on the fruit from each sample collection site. A total of 15 samples were collected from each variety, and a total of 195 fruit samples were collected. The samples were firstly placed in an insulated foam box with an ice bag and transported back to the laboratory. The samples were then frozen in a refrigerator at −15 ℃. A systematic measurement was performed on the fruit quality and medicinal component indexes (soluble solids, protein, total sugar, total acid, vitamin C, trace elements, total flavonoids, anthocyanins, β-carotene, lycopene, and amino acids, fatty acids). A comprehensive evaluation was then made to calculate the total score. The results showed that there were various degrees of the differences in the contents of various nutrients and medicinal components in the fruits of 13 tested seabuckthorn varieties. The physical and chemical indexes of seabuckthorn in Qinghe county were 0.93-5.54 times,0.90-4.49 times, 0.99-13.67 times, and 1.10-4.98 times higher than those in Buerjin, Habahe, Wushi, and Aheqi county, respectively. Among them, the contents of vitamin C, anthocyanin, and lycopene in the fruits of seabuckthorn in Qinghe county were significantly different from those in the rest regions. The β-carotene content of seabuckthorn fruit in Qinghe county was 6.2 and 3.03 times higher than that in Wushi and Aheqi county, respectively. The highest comprehensive score was the 'Zhuangyuanhuang' fruit in Qinghe county, whereas, the 'Wucifeng' was the lowest. The comprehensive score of fruit was also calculated by factor analysis. The average comprehensive score of 'Zhuangyuanhuang' was the highest, followed by 'Shenqiuhong' and 'Wucifeng'. Qinghe county shared the highest average comprehensive score, followed by Burqin, Habahe, Aheqi, and Wushi County, in terms of spatial distribution. In summary, the Altay area can achieve in the optimum growth and development of seabuckthorn, indicating the best quality.