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The fungal genus Trichoderma has been extensively studied due to its role in the mycoparasitism, and thus developed as biocontrol agent against various plant pathogens. Although the mycoparasitic processes of several Trichoderma species have already been well understood, the information about the mycoparasitic mechanisms of Trichoderma strains resulted from different growth conditions or interacting with different phytopathogens is still limited. In this study, we utilized transcriptome sequencing to identify the differentially expressed genes (DEGs) at 0, 24, 72 and 120 h from T. atroviride strain SS003, growing on an induced-medium with cell walls of Pinus armandii pathogen Cronartium ribicola (CRCW). In total, 86,155,316 reads were obtained with 43,077,658 clean reads. Further, 10,422 genes were identified from four transcriptomes and accounted for 93.89% of annotated genes in T. atroviride IMI 206040 genome, reflecting high-quality sequencing and assembly. In each pairwise comparison, a large number of DEGs were identified with different numbers of genes for up- and down-regulation, respectively. In the presence of CRCW, expression of two main glycoside hydrolase gene families (i.e. chitinase and glucosidase) was induced. Most of 14 secreted enzymes by quantitative real time PCR (qPCR) analysis exhibited a consistent expression pattern with that by RNA-Seq data. This comparative study leads to the identification of phase-specific genes in the interactions of T. atroviride SS003 with C. ribicola, and provides potential molecular targets for improved biocontrol strategies.