The fungal Trichoderma has been extensively studied due to its role in the mycoparasitism, and thus developed as biocontrol agents against various plant pathogens. Although the mycoparasitic process of several Trichoderma species was already well understood, the information on the mycoparasitic mechanisms of different growth conditions or interacting with different phytopathogens is still lacked. To enhance our knowledge and identify differentially expressed genes (DEGs) of the mycoparasitism on Trichoderma atroviride strain SS003 against Pinus armandii pathogen Cronartium ribicola, here we utilized transcriptome sequencing to identify the DEGs at 0, 24, 72 and 120 h from T. atroviride strain SS003, growing on an induced-medium with the cell walls of C. ribicola (CRCW). Such study will provide potential molecular targets for improved biocontrol strategies.