The invention relates to the technical field of microorganisms, in particular to a method for preparing a metabolite for controlling tobacco mosaic virus disease and its application. The invention provides a Trichoderma harzianum LTR-2 to control tobacco mosaic virus disease, more specifically application of Trichoderma harzianum LTR-2 metabolites in the control of tobacco mosaic virus disease. The invention obtains a strain for controlling tobacco mosaic virus disease from Trichoderma spp. stored in laboratory, and carries out virus control research on the metabolite of the strain so as to directly and rapidly control tobacco mosaic virus disease, ensure tobacco yield and quality, and provide reference for maintaining microbial community balance in tobacco planting.