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<i>Ectropis obliqua</i> is a destructive masticatory pest in China’s tea gardens. <i>Beauveria bassiana</i> as microbial insecticides can effectively control <i>E. obliqua</i> larvae; however, the immune response of this insect infected by <i>B. bassiana</i> are largely unknown. Here, after isolating a highly virulent strain of <i>B. bassiana</i> from <i>E. obliqua</i>, the changes in gene expression among different tissues, including hemocytes and fat bodies, of <i>E. obliqua</i> larvae infected by the entomopathogen were investigated using transcriptome sequencing. A total of 5877 co-expressed differentially expressed genes (DEGs) were identified in hemocytes and fat bodies, of which 5826 were up-regulated in hemocytes and 5784 were up-regulated in fat bodies. We identified 249 immunity-related genes, including pattern recognition receptors, immune effectors, signal modulators, and members of immune pathways. A quantitative real-time PCR analysis confirmed that several pattern recognition receptors were upregulated in hemocytes and fat bodies; however, others were downregulated. The investigated immune effectors (<i>ATT</i> and <i>PPO-1</i>) were suppressed. The results showed that there were tissue differences in the expression of immune genes. This study provides a large number of immunity-related gene sequences from <i>E. obliqua</i> after being infected by <i>B. bassiana</i>, furthering the understanding of the molecular mechanisms of <i>E. obliqua</i> defenses against <i>B. bassiana</i>.