Abstract: To investigate the the role of polyphenols in determining the quality of upper tobacco leaves from Sichuan and to elucidate their intrinsic relationship with the flavor types of flue-cured tobacco, the contents of major polyphenols in upper leaves with three flavor types—fresh-sweet, mellow-sweet, and honey-sweet—were systematically characterized using multivariate statistical analysis. The results showed that rutin and chlorogenic acid were highly significantly positively correlated with tobacco leaf quality, while scopoletin was highly significantly negatively correlated with quality. The polyphenol composition of fresh-sweet flavor tobacco leaves differed significantly from that of honey-sweet and mellow-sweet flavor leaves, while only minor differences were observed between the latter two flavor types. Rutin (VIP = 1.22) was identified as the key polyphenol discriminating among different flavor types of upper tobacco leaves from Sichuan, showing higher levels in fresh-sweet flavor leaves and lower levels in honey-sweet and mellow-sweet flavor leaves. In summary, rutin serves as an important polyphenol marker distinguishing fresh-sweet flavor tobacco leaves from the other two flavor types. Rutin, chlorogenic acid, and scopoletin are key polyphenols influencing the quality of upper tobacco leaves in Sichuan, with rutin and chlorogenic acid showing significantly higher level in the Liangshan and Panzhihua regions than the other producing areas.