We previously reported that cyclophilin A (CyPA) production is upregulated in preeclampsia (PE). Moreover, CyPA is known to induce PE-like features in pregnant mice and impair trophoblast invasiveness. In this study, we further illustrated the role of CyPA in PE. RNA-seq analysis, RT-qPCR, immunohistochemical (IHC) staining, and western blotting of mouse placentae revealed that CyPA increased the levels of extracellular matrix (ECM) proteins, such as collagen I and fibronectin, and activated the TGF-β/Smad3 signaling pathway. Additionally, CyPA inhibited the expression of genes involved in epithelial-mesenchymal transition (EMT) (e.g., E-cadherin, N-cadherin, and vimentin) in mouse placentae. We then constructed stable overexpressing and knock-down CyPA cell models (using HTR8/SVneo cells) to clarify the molecular mechanism. We found that CyPA regulated the levels of ECM-related proteins and the EMT process through the TGF-β/Smad3 pathway. We also identified SERPINH1 as a putative CyPA-binding protein, using liquid chromatography-electrospray mass spectrometry (LC-MS)/MS. SERPINH1 was found to be upregulated in the placentae of PE. Silencing SERPINH1 expression reversed the upregulation of ECM proteins and inhibition of the EMT process induced by the overexpression of CyPA. These findings revealed the functions of CyPA in the impaired invasiveness of trophoblasts in PE and indicated that CyPA and SERPINH1 may represent promising targets for the treatment of PE.