Porcine circovirus type 2 (PCV2) has been a notorious killer for the pig industry, causing substantial economic losses worldwide. However, its pathogenesis is still poorly understood. Comparative transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) were performed in different porcine tissues after PCV2 infection. Our comparative transcriptomic analysis obtained 40 key differentially expressed genes (DEGs), and our WGCNA identified 458 hub genes. Significantly, both TPX2 microtubule nucleation factor (TPX2) and Aurora kinase A (AURKA) are included in these key DEGs and hubs genes. Our gene ontology (GO) analysis indicated that the key DEGs and hub genes participated in cell cycle regulation and immune response. The expressive levels of TPX2 and AURKA went down in the spleen but up in the kidneys after infection with PCV2. We conclude that TPX2 and AURKA played an essential role in PCV2 infection.