In order to optimize the grading structure, improve the industrial availability of upper tobacco leaves and economic benefit of flue-cured tobacco, a field experiment was conducted to investigate the effects of removing 6 inapplicable lower leaves and spraying micronutrient fertilizer on the agronomical character, chlorophyll content, photosynthetic characteristics, carbon and nitrogen metabolism, conventional chemical composition and economic traits of flue-cured tobacco (Nicotiana tabacum cv. ‘Yuyan No.6’). The results showed that the treatment with removing 6 inapplicable lower leaves after topping significantly enhanced the leaf area, chlorophyll content, photosynthesis, carbon and nitrogen metabolism, and remarkably increased the total nitrogen and nicotine contents of upper tobacco leaves, decreased reducing sugar contents, the ratio of total sugar to nicotine and the output value of flue-cured tobacco when compared to the treatments without removing inapplicable lower leaves and removing 4 inapplicable lower leaves. Compared to only removing 6 inapplicable leaves, combination of removing 6 inapplicable leaves and spraying micronutrient fertilizer further promoted the growth of upper leaf, significantly increased reducing sugar contents, the ratio of total sugar to nicotine, potassium content and the output value of flue-cured tobacco, and remarkably reduced the nicotine contents of upper leaves. Compared to the treatment without removing inapplicable lower leaves, combination of removing 6 inapplicable leaves and spraying micronutrient fertilizer increased the leaf area, single leaf weight, potassium content, the ratio of potassium to chlorine, and the proportion of superior and middle grading leaves by 10.66%, 16.49%, 13.43%, 18.27% and 15.00%, respectively. In general, combination of removing 6 inapplicable leaves and spraying micronutrient fertilizer can promote the upper leaf unfolding, improve the grading structure and quality, and increase the economic benefits of flue-cured tobacco.