Biocontrol is becoming an increasingly prevalent pest management strategy in agricultural systems, and the biocontrol fungal strain Trichoderma harzianum T-22 has been widely used in combating different plant diseases. Phytophthora capsici, a destructive oomycete pathogen, can infect a broad range of hosts and cause huge economic losses. A previous study found that T. harzianum T-22 can effectively inhibit P. capsici, and a large number of glycoside hydrolase (GH) encoding genes were upregulated during T. harzianum-P. capsici interaction. In the current study, the GH family was characterized and the expression pattern of six interaction induced genes (ThIIGH1-6) was determined by qPCR analysis. To investigate the function of key genes for biocontrol efficacy, a robust gene knock-out strategy was established and four genes (ThIIGH1-4) encoding putatively secreted proteins were successfully knocked out. Biological characteristic assays showed that deletion of these genes did not affect basal growth or development of T. harzianum. However, the ThIIGH1 and ThIIGH3 knock-out mutants displayed significantly decreased inhibitory activity against P. capsici. Cell wall hydrolase activity assays suggested that the biocontrol impairment of the mutants is mainly caused by the reduction of cellulase activity. Moreover, ThIIGH1 and ThIIGH3 were independently overexpressed in T. harzianum, which resulted in genetic engineering strains with higher inhibitory activity against P. capsici. Our results demonstrate a direct functional link between the target genes and the mechanisms essential for biocontrol. The genetic transformation system developed for T. harzianum thereby serves as a robust platform for advancing gene function study and strain improvement.