Lycium barbarum L. (LBL) is an important medicinal and edible plant, has been used in China for more than 2,000 years as a traditional medicinal herb and food supplement. Currently, LBL has been cultivated in the Northwest of China like Ningxia, Qinghai, Inner Mongolia, Gansu and Xinjiang province. With the expanding of plantation areas and developing of new varieties, more and more factors affecting qualities of LBL, to establishing a quality evaluation method based on both commercial quality and effective components is very essential. The purpose of this study was to investigate the correlation between the phenotype and main nutritional functional components of LBL, and to construct a comprehensive quality evaluation system for LBL, to provide reference for the quality evaluation of LBL for both medicinal and edible use. Taking 224 of LBL samples including different batches, grades, germplasm and origin as research objects, the correlation between phenotype characteristics and chemical composition of LBL was studied, and PCA, hierarchical analysis and discriminant analysis were used to comprehensive quality evaluate of LBL. The results showed that the content of nutritional efficacy components of LBL was highly correlated with phenotypic characteristics. The smaller the LBL fruit is (i.e. the smaller the longitudinal area, longitudinal diameter, transverse diameter and average fruit weight), the higher the content of effective components such as Lycium barbarum polysaccharide, betaine and carotenoids are, but lower the total sugar content is. LBL for both medicinal and food use can be evaluated and classified by four functional components including Lycium barbarum polysaccharide, flavonoid, betaine, carotenoid and two phenotypic indexes including longitudinal diameter and a value. The quality evaluation method for LBL established in this paper can provide reference for comprehensive quality evaluation. The established discriminant function for the comprehensive quality of LBL has high accuracy, which can be used to discriminate the comprehensive quality of LBL for both medicine and food use, and provide reference for the breeding of new varieties of LBL.