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<i>Verticillium dahliae</i> is a soilborne fungal pathogen that causes vascular wilt diseases in a wide range of economically important crops, including eggplant. <i>Trichoderma</i> spp. are effective biological control agents that suppress a wide range of plant pathogens through a variety of mechanisms, including mycoparasitism. However, the molecular mechanisms of mycoparasitism of <i>Trichoderma</i> spp. in the degradation of microsclerotia of <i>V. dahliae</i> are not yet fully understood. In this study, the ability of 15 isolates of <i>Trichoderma</i> to degrade microsclerotia of <i>V. dahliae</i> was evaluated using a dual culture method. After 15 days, isolate HZA14 showed the greatest potential for microsclerotial degradation. The culture filtrate of isolate HZA14 also significantly inhibited the mycelial growth and conidia germination of <i>V. dahliae</i> at different dilutions. Moreover, this study showed that <i>T. virens</i> produced siderophores and indole-3-acetic acid (IAA). In disease control tests, <i>T. virens</i> HZA14 reduced disease severity in eggplant seedlings by up to 2.77%, resulting in a control efficacy of 96.59% at 30 days after inoculation. Additionally, inoculation with an HZA14 isolate increased stem and root length and fresh and dry weight, demonstrating plant growth promotion efficacy. To further investigate the mycoparasitism mechanism of <i>T. virens</i> HZA14, transcriptomics sequencing and real-time fluorescence quantitative PCR (RT-qPCR) were used to identify the differentially expressed genes (DEGs) of <i>T. virens</i> HZA14 at 3, 6, 9, 12, and 15 days of the interaction with microsclerotia of <i>V. dahliae</i>. In contrast to the control group, the mycoparasitic process of <i>T. virens</i> HZA14 exhibited differential gene expression, with 1197, 1758, 1936, and 1914 genes being up-regulated and 1191, 1963, 2050, and 2114 genes being down-regulated, respectively. Among these genes, enzymes associated with the degradation of microsclerotia, such as endochitinase A1, endochitinase 3, endo-1,3-beta-glucanase, alpha-N-acetylglucosaminidase, laccase-1, and peroxidase were predicted based on bioinformatics analysis. The RT-qPCR results confirmed the RNA-sequencing data, showing that the expression trend of the genes was consistent. These results provide important information for understanding molecular mechanisms of microsclerotial degradation and integrated management of <i>Verticillium</i> wilt in eggplant and other crops.