T cell exhaustion is a state of T cell dysfunction during chronic infection and cancer. Antibody-targeting immune checkpoint inhibitors to reverse T cell exhaustion is a promising approach for cancer immunotherapy. However, molecular mechanisms of T cell exhaustion remain incompletely understood. Here, we performed a transcriptome analysis by integrating seven exhaustion datasets caused by multiple diseases in both humans and mice. In this study, an overlap of 21 upregulated and 37 downregulated genes was identified in human and mouse exhausted CD8+ T cells. These genes were significantly enriched in exhaustion response-related pathways, such as signal transduction, immune system processes, and regulation of cytokine production. Gene expression network analysis revealed that the well-documented exhaustion genes were defined as hub genes in upregulated genes. In addition, a weighted gene co-expression analysis identified 175 overlapping genes that were significantly correlated with the exhaustion trait in both humans and mice. This study found that overlapping six genes were significantly upregulated and highly related to T cell exhaustion. Finally, we revealed that CD200R1 and ADGRG1, less described previously in exhaustion, contributed to T cell exhaustion. Overall, our findings reveal the mechanisms of T cell exhaustion and provide an important reference to the immunology community.