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Fusarium wilt is one of the important soil borne diseases of various crops, and spores or disease residues can survive in the soil for a long time, making it difficult to control and causing great harm to agricultural production. In order to provide ideas and data support for the further analysis of the mechanism of two ethanol extracts of clove and licorice inhibiting Fusarium wilt, in this experiment, the effects of two plant extracts on the gene expression level of Fusarium oxysporum by transcriptome high-throughput sequencing were further analyzed and studied. The results showed that the sequencing error rates were all less than 0.025%, and there was a significant difference in correlation coefficients between within and between sample groups. Therefore, the sequencing data had high accuracy and good biological repeatability. After treatment with licorice extract, differential genes were mainly enriched in the GO database in the membrane components and intrinsic component, and 53.27% of the differential genes involved in these pathways were upregulated. The phenylalanine metabolism pathway was most significantly enriched in the KEGG pathway. After treatment with clove extract, the pathways significantly enriched in the GO database were the same as those of licorice, and 33.98% of the differentially expressed genes involved in these pathways were upregulated. The KEGG pathway showed the most significant enrichment of differentially expressed genes in the purine metabolism pathway. Research showed that the main antibacterial mechanism of licorice extract against Fusarium oxysporum may be to promote the generation and metabolism of various components of fungal cell membrane at the translation level, simultaneously reducing the damage repair function of Fusarium oxysporum DNA and the generation and metabolism level of nutrients such as amino acids. The effect of clove extract on Fusarium oxysporum may lead to overexpression of genes involved in mycelial cell growth or resistance mechanisms, vigorous RNA metabolism, and promotion of cell membrane growth and metabolism, resulting in abnormal mycelial growth. In summary, it could be seen that the two plant extracts with significant antibacterial effects probably had different antibacterial mechanisms against the same species of Fusarium oxysporum. [ABSTRACT FROM AUTHOR]