Abstract:[Objective] This paper aimed to analyze the role of TvRpd3 encoding histone deacetylase in the biocontrol of Trichoderma viride Tv-1511 by constructing the engineered strain with TvRpd3 deleted (∆TvRpd3). [Methods] Fusion PCR technique and homologous recombination method were employed to delete TvRpd3 in T. viride Tv-1511. Confrontation culture, phenotype observation, immunohistochemistry detection, and metabonomics analysis were carried out to compare the histone acetylation level, secondary metabolite synthesis, antagonism to pathogens, and field biocontrol effect between the engineered and the wild-type strains. [Results] Compared with the wild type, ∆TvRpd3 exhibited enhanced inhibitory effects on pathogens. The biocontrol effects of ∆TvRpd3 fermentation broth on wheat powdery mildew, tobacco black shank, and tomato Fusarium wilt increased by 62.27%, 57.45%, and 70.71%, respectively. Meanwhile, the knockout of TvRpd3 significantly changed the species and yields of secondary metabolites produced by Trichoderma. Specifically, the yields of several vital antibiotic substances including trichomycin, sorbicillinoids, and monocillin I produced by ∆TvRpd3 increased compared with those of the wild type. [Conclusion] TvRpd3 mediates histone deacetylation to play a role in the biocontrol of T. viride.