Comprehensive evaluation of the free amino acid composition of 28 different varieties of lotus rhizomes was carried out by correlation analysis, principal component analysis (PCA) and cluster analysis. Results showed that a total of 17 free amino acids were identified. The average contents of essential amino acids, non-essential amino acid and total free amino acids were 2.05, 12.27 and 14.33 mg/g, respectively. PCA showed that the first three principal components accounted for 80.16% of the total variance, really reflecting comprehensive information on free amino acids in lotus rhizomes. The top five varieties with the highest comprehensive scores were ‘Jinhuawuziou’, ‘Xibo’, ‘E’lian 5’, ‘Wuyibaimushiyong’ou’ and ‘Jinhuahonglian’. Cluster analysis showed the 28 cultivars were divided into three groups, which was consistent with the results of PCA. This study can provide a theoretical basis for further lotus breeding, quality improvement, processing and storage.