The lives of ovarian cancer patients are threatened largely due to metastasis and drug resistance. Endogenous peptides attract increasing attention in oncologic therapeutic area, a few anti-tumor peptides have been approved by the food and drug administration (FDA) for clinical use over the past decades. However, only few peptides or peptide-derived drugs with anti-ovarian cancer effects have been identified. Here we focused on the biological roles and mechanism of a peptide named PDHPS1 in ovarian cancer development. Our results indicated that PDHPS1 reduced the proliferation ability of ovarian cancer cells in vitro and inhibited the ovarian cancer growth in vivo. Peptide pull down and following mass spectrometry, western blot and qRT-PCR revealed that PDHPS1 could bind to protein phosphatase 2 phosphatase activator (PTPA), an essential activator of protein phosphatase 2A (PP2A), which resulted in increase of phosphorylated YAP, further inactivated YAP and suppressed the expression of its downstream target genes. Flow cytometry, cell membrane permeability test and immunohistochemical staining study demonstrated that there are no observable side effects of PDHPS1 on normal ovarian epithelium and hepatorenal function. Besides, modification of membrane penetration could improve the physicochemical properties and biological activity of PDHPS1. In conclusion, our study demonstrated that the endogenous peptide PDHPS1 serves as an anti-tumor peptide to inhibit YAP signaling pathway though interacting with PTPA in ovarian cancer.