Abstract: The purpose of this paper was to clarify the reasonable application method of magnesium fertilizer in the tobacco-growing areas of Fujian province, in order to provide guidance for the improvement of tobacco quality. Cuibi No.1 was used as the experimental material, and the field randomized block experiment was carried out with no magnesium fertilizer as the control. Then, the effects of magnesium fertilizer application methods such as the basal application, top dressing, hole application combined with top dressing, hole application combined with spraying in the critical periods on the agronomic traits, biomass, average weight per leaf, chemical composition, economic traits and sensory evaluation quality of flue-cured tobacco were studied. The results showed that the basal application promoted the growth of tobacco plants at the seedling stage, increased the average weight per leaf, and significantly reduced the total nitrogen content and the proportion of nitrogen to nicotine in the upper and lower leaves. Top dressing promoted the growth of stem and reduced the contents of total nitrogen and reducing sugar in the upper and lower leaves. The combination of hole application and top dressing was beneficial to the synthesis of carbohydrates in the leaves, which was not conducive to the nicotine biosynthesis in the later stage of growth; the combination of hole application and spraying in the critical period significantly promoted the growth of leaves in the later stage of growth, and the proportion of the middle-grade and upper-grade tobacco leaves increased by about 10%, and the characteristics such as aroma, smoke and taste of the flue-cured tobacco leaves were the best. The method of hole application combined with spraying in the critical period should be recommended for the input of magnesium fertilizer in the tobacco-growing areas of Fujian province, which could effectively highlight the style of local tobacco leaves, improve the quality of tobacco leaves, and promote the healthy development of industry.