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Flavonoids are crucial secondary metabolites that possess the ability to mitigate UV damage and withstand both biotic and abiotic stresses. Therefore, it is of immense significance to investigate the flavonoid content as a pivotal indicator for a comprehensive assessment of chestnut's drought tolerance. This study aimed to determine the flavonoid content and drought tolerance-related physiological and biochemical indices of six chestnut varieties (clones) grafted trees—Qianxi 42 (QX42), Qinglong 45 (QL45), Yanshanzaofeng (YSZF), Yanzi (YZ), Yanqiu (YQ), and Yanlong (YL)-under natural drought stress. The results were used to comprehensively analyze the drought tolerance ability of these varieties. The study revealed that the ranking of drought tolerance indices in terms of their ability to reflect drought tolerance was as follows: superoxide (oxide) dismutase (SOD) activity, ascorbate peroxidase (APX) activity, flavone content, catalase (CAT) activity, proline (PRO) content, soluble sugar content, peroxidase (POD) activity, betaine content, flavonol content, hydrogen peroxide (H2O2) content, soluble protein content, superoxide ion (OFR) content, superoxide (ion OFR) production rate, malondialdehyde (MDA) content, chlorophyll content. Through principal component analysis, the contents of flavonoids and flavonols can be used as indicators for comprehensive evaluation of drought tolerance of chestnut. The comprehensive evaluation order of drought tolerance of grafted trees of 6 chestnut varieties (Clones) was: QL45 > QX42 > YQ > YZ > YSZF > YL. [ABSTRACT FROM AUTHOR]