The invention relates to the technical filed of fertilizer for tobacco and discloses trace element fertilizer for the tobacco as well as a preparation method and an application method of the trace element fertilizer. The fertilizer comprises magnesium sulfate heptahydrate, zinc sulfate, boric acid, monopotassium phosphate and water, is used in a rosette stage and a vigorous growth stage of the tobacco and can improve the resistance of flue-cured tobacco remarkably, enhance the disease resistance, improve the tobacco aroma and increase the proportion of first-class and medium-class tobacco, thereby improving the quality of the tobacco. The fertilizer has the advantages of simple components, exact fertilizer efficiency, a little use amount, high absorptivity, low cost and high earnings and has great economic significance in agricultural development.