The invention discloses a special trace element fertilizer formula for tobacco and a preparation method thereof. The formula comprises the following components: 0.25-0.5kg of borax, 0.25-0.5kg of zinc sulfate, 0.025-0.05kg of ammonium molybdate and 0.5kg of potassium fulvate. The preparation method of the fertilizer formula comprises the following steps of separately weighing the fertilizers such as borax, zinc sulfate, ammonium molybdate and potassium fulvate according to the fertilizer mass percentage of 0.25-0.5kg of borax, 0.25-0.5kg of zinc sulfate, 0.025-0.05kg of ammonium molybdate and 0.5kg of potassium fulvate per mu of tobacco; sufficiently and uniformly stirring the weighed borax, zinc sulfate, ammonium molybdate and potassium fulvate in 50kg of clear water to prepare a solution of the special trace element fertilizer for tobacco; performing foliage spray for tobacco. In the invention, through the foliage spray for tobacco, the current situation that the growth and development and quality of tobacco are influenced by insufficient trace elements of soil is effectively improved, the content of trace elements in the tobacco leaves is increased, conventional chemical components of tobacco leaves are improved, and the aroma of the tobacco leaves is increased; moreover, the tobacco quality is improved, and the drop of tobacco quality caused by inefficiency in the trace elements of soil is effectively relieved.