According to severe boron-deficiency characteristics of tobacco-growing soil in karst Wenshan, we proposed a resolution of boron application to improve yield and quality of tobacco. A field experiment was conducted with flue-cured tobacco variety ‘Yunyan 100' as material, and borax was the source of boron fertilizer. The effects of basal application and foliar spraying borax fertilizer on soil, vegetative growth, photosynthetic characteristics, yield and quality of flue-cured tobacco were studied. The results showed that compared with CK treatment, basal application or spraying of boron fertilizer had no significant effect on soil pH, organic matter, hydrolyzed nitrogen, available phosphorus, available potassium and water-soluble chlorine contents, but could significantly increase soil available boron content. Moreover, it could promote the vegetative growth, superior proportion, yield and output value of tobacco, among which the output value in T5, T6 and T8 treatments increased by 24.57%, 21.59% and 28.15% compared with T1(CK), respectively. Similarly, compared with CK treatment, net photosynthetic rate (Pn), stomatal conductance (Gs) and intercellular CO2 concentration (Ci) of tobacco leaves were significantly increased by 10.22%-90.11%, 18.17%-90.91% and 6.56%-51.97%, respectively, particularly in T5, T6 and T8 treatments. Meanwhile, the transpiration rates (Tr) of T2, T3, T5, T6 and T8 were significantly reduced by 2.78%-26.85%. Compared with CK, boron application treatments significantly improved the content of total sugar, reducing sugar, total nitrogen, nicotine, potassium oxide, water-soluble chlorine, calcium, magnesium and boron, and T5, T6 and T8 tobacco leaves had the best chemical composition coordination. On the boron-deficient tobacco-growing soil in the karst area of Wenshan, the integration of basal application and spraying borax fertilizer could significantly increase the content of available boron in soil and tobacco leaf, and effectively promote growth, photosynthetic rate, yield, economic benefits, and coordination of chemical composition of flue-cured tobacco. In summary, it was best to apply 15-22.5 kg/hm2 of basal borax application combined with spraying borax at 0.1%, 0.2% and 0.3% at resettling stage, vigorous growing stage, maturing stage, respectively.