This study aimed to clarify the effects of different leaf identities and leaf structures on the chemical components, macromolecular substances, physical properties, appearance quality and sensory quality of upper tobacco leaves, and to screen the optimal phenotypic characteristics of high-quality and high-yield upper tobacco leaves. Taking the upper leaves of the dominant flue-cured tobacco cultivar ‘Yunyan 87’ in Huidong tobacco-growing area, Liangshan, Sichuan Province as research materials, this study systematically analyzed the variations in chemical components, macromolecular substances, physical characteristics, appearance scores and sensory quality in response to diverse leaf identities and leaf structures. Correlation analysis and redundancy analysis were further applied to reveal the correlation relationships among these indicators. The results showed that leaf identity had a greater influence on the chemical composition, macromolecular substances, and physical properties of upper tobacco leaves than leaf structure. Compared with medium-identity leaves, the nitrogen and nicotine contents in upper leaves with thick identity significantly increased by 13.94% and 36.57%, respectively, while the contents of reducing sugar, chlorine, and cellulose significantly decreased by 12.65%, 53.57%, and 15.56%, respectively. Starch content in upper leaves with compact structure significantly increased by 27.22% compared with that in leaves with loose structure. Compared with medium-identity leaves, leaves with thick identity exhibited significant increases in leaf width, single leaf weight, leaf thickness, and leaf surface density by 21.36%, 62.94%, 43.23%, and 39.07%, respectively, while stem percentage significantly decreased by 24.95%. The upper leaves with slightly thick identity achieved the highest appearance and sensory scores, and those with loose structure also obtained high appearance and sensory ratings. Upper leaves characterized by slightly thick identity and loose structure exhibited superior quality and enhanced industrial usability. Therefore, leaf identity should be regarded as a key indicator in the industrial selection and processing of high-quality upper tobacco leaves. Subsequent studies could be conducted on multi-cultivar comparison, cross-regional verification and physiological and molecular mechanisms. Meanwhile, an intelligent grading model based on leaf appearance characteristics can be constructed, so as to provide systematic technical support for high-quality tobacco leaf production and the improvement of industrial usability in Sichuan tobacco-growing areas.