The invention belongs to the field of agricultural planting industry and particularly relates to tobacco base fertilizer and an application method thereof. The tobacco base fertilizer contains various nutrient elements including nitrogen, phosphorus, kalium, chlorine and sulfur, wherein the weight ratio of the nitrogen to the phosphorus to the kalium to the chlorine to the sulfur is 9:10:26:0.8-1.2:5. The application method of the tobacco base fertilizer has the advantages that farmyard manure is applied during flue-cured tobacco field soil preparation and compartment arrangement, then, oil cake is applied to nests, flue-cured seedlings are transplanted, and finally the tobacco base fertilizer is annularly applied to the periphery of the flue-cured seedlings. The tobacco base fertilizer is adopted when the flue-cured seedlings are transplanted and has the advantages of improving the yield per mu and lowering floral leaf plant diseases and insect pests.