In order to explore the phenotypic diversity of wild Hippophae rhamnoides subsp. Sinensis resources in Qinghai Province, 150 wild Seabuckthorn resources from 10 regions in Qinghai Province were collected and 12 phenotypic traits were analyzed. The results showed that Seabuckthorn had rich phenotypic diversity in Qinghai Province, the coefficient of variation of 12 phenotypic characters ranged from 16.49% to 58.76%. Among them, ground diameter, tree height and thorn length had great variation, and the coefficient of variation was over 50%. Correlation analysis showed that there were significant or extremely significant correlations among all characters except tree height, branch, ground diameter and leaf width. At the same time, the phenotypic traits of Seabuckthorn were correlated with latitude and altitude, and different traits were affected by different geographical factors, among which the leaf traits were the most affected. Four principal components with eigenvalues greater than 1 were selected by principal component analysis, and the cumulative contribution rate was 86.35%, which contained most of the information about phenotypic traits of Seabuckthorn. Fruit weight had the greatest effect on phenotypic traits diversity of Seabuckthorn. The results of cluster analysis showed that at 15 Euclidean distances, the tested materials could be divided into three groups. These results indicate that the phenotypic characters of Seabuckthorn resources in Qinghai are rich in diversity and have great potential for exploitation and utilization. This study provided a scientific basis for the breeding and preservation of excellent germplasm resources of Hippophae rhamnoides subsp. Sinensis.