[Objective] To identify the candidate genes and second metabolites involved in NaCl stress response of Trichoderma harzianum ACCC32524, thereby exploring the mechanism of NaCl stress adaptation.[Methods] The transcriptomes of ACCC32524 with the treatment of 0, 0.4, 0.6 mol/L NaCl were compared using Illumina HiSeq XTen high-throughput sequencing and the metabolomes with the treatment of 0, 0.6 mol/L were detected by GC-TOF-MS. The annotation, screening and classification of differentially expressed genes (DEGs) and secondary metabolites were completed by using related softwares and databases. Validation of DEGs using RT-qPCR.[Results] A total of 417 and 733 DEGs were found of ACCC32524 with the treatment of 0.4 or 0.6 mol/L NaCl respectively. GO analysis suggested that total of 318 and 582 DEGs were categorized into three functional classifications (biological process, molecular function, cellular component) and forty sub-categories; COG classification results showed that 232 and 414 transcripts were assigned to the same 20 categories and these transcripts were significantly enriched in various known amino acid transport and metabolism, general function prediction only and carbohydrate transport and metabolism; KEGG pathway analysis revealed that filtered 79 and 96 DEGs were enriched in 25 individual pathways, and those genes were significantly enriched in biosynthesis of amino acids and 2-oxocarboxylic acid metabolism pathways. A total of 22 genes were screened from transcriptome data related with osmotic regulation, ion transport and ROS scavenging. A total of 101 differential secondary metabolites were screened from the metabolome data under 0.6 mol/L NaCl stress, including 8 upregulated and 93 downregulated substances, 36 of which were qualitatively identified and distributed in 9 classifications, such as carbohydrates, organic acids and amino acids. The expression level of selected DEGs was tested with RT-qPCR, and they were consistent with the result of RNA-seq analysis.[Conclusion] Under NaCl stress, a large number of genes and secondary metabolites of Trichoderma harzianum ACCC32524 were changed and the metabolic pathway was significantly shifted. These processes together reduced the toxicity of salt ions to cells and enhanced the tolerance of strains to salt stress. This study further provided the gene information for the research of salt tolerance mechanism of Trichoderma spp..