The invention relates to the field of microbial control, in particular to bacillusamyloliquefaciens subsp Lh-1 and application thereof. With a preservation number of CGMCC No.8548, the bacillusamyloliquefaciens subsp Lh-1 is applied in control of Verticillium dahliae, erwinia carotovora, ralstonia solanacearum, valsa leucostoma, Valsa Mali Miyabe et Yamada, Phytophthora capsici and phytophthora infestans. According to the invention, the bacillusamyloliquefaciens subsp Lh-1 and pesticide and chitosan oligosaccharide with dual effects of fertilizer and pesticide are combined into an Lh-1 microecological agent, the viable count is small, the dosage is small, the production process is simple, the cost is low, and the Lh-1 microecological agent has the dual functions of disease prevention and growth promotion. Nursery test proves that reduce the disease incidence of crop is reduced, especially for control of Verticillium dahliae, the disease incidence drops to 6%, and the control effect is significant. In addition, the Lh-1 microecological agent is a biological strain preparation, is completely free of a series of problems caused by use of chemical pesticides, thus being conducive to pollution-free production of crops, and farmers can have no need for pesticide or reduce the dosage of chemical pesticide, thus greatly saving the expenditure.