As an important oil and economic crop in arid and semi-arid regions of China, studying the genetic diversity of flax germplasm resources is of great significance for flax breeding. In this study, 525 flax germplasm resources from domestic and foreign sources were integrated, and 17 major phenotypic traits were systematically analyzed through two consecutive years of planting and identification. The results showed that the variation of petal color was the most abundant, while traits such as seed coat color and stem base shape were dominated by single phenotypes; the coefficient of variation of grain weight per plant, capsule number per plant and 1000-seed weight all exceeded 20%, indicating great potential for improvement; the coefficient of variation of capsule diameter, oil content and protein content was relatively low, which were the core conservative traits of flax varieties. Correlation analysis showed that there were significant or highly significant positive and negative correlations among multiple traits. 1000-seed weight and grain weight per plant were highly significantly positively correlated with capsule diameter and oil content, while plant height and technical length were highly significantly negatively correlated with 1000-seed weight and grain weight per plant; linolenic acid content was highly significantly positively correlated with protein content. Cluster analysis divided the 525 flax germplasm resources into four distinct groups. Group Ⅰ was the core germplasm for breeding high-linolenic acid oil flax; Group Ⅱ provided a special material pool for the breeding of early-maturing and high-oil flax varieties; Group Ⅲ was the ideal basic material for breeding fiber-oil dual-purpose flax varieties; Group Ⅳ was the key germplasm for broadening the genetic basis and mining excellent genes of flax. Principal component analysis extracted five principal components with a cumulative variance contribution rate of 73.47%. The comprehensive evaluation F-value ranged from 0.382 to 0.608, with an average of 0.486, and ten excellent germplasms including “Xinjiangbai” (F=0.698) were screened out. The F-value was significantly correlated with 13 key traits. This study systematically clarified the phenotypic genetic diversity characteristics, trait correlation rules and cluster differentiation characteristics of 525 flax germplasm resources, which provided abundant materials and clear directions for flax breeding, and laid a foundation for further broadening the genetic basis of flax and providing sustainable technical support for the high-quality development of the industry.