Ovarian cancer is a serious gynecological malignancy, and early identification of prognostic markers is critical to improve clinical outcomes. Aquaporin 5 (AQP5) and cell cycle regulatory protein CTDP1 are considered as potential prognostic protein markers, but their specific molecular structure and immune function have not been thoroughly studied. The aim of this study was to investigate the molecular structure of AQP5 and CTDP1 and their immune function in ovarian cancer, to evaluate their potential as prognostic markers, and to provide new ideas for the diagnosis and efficacy monitoring of ovarian cancer. Cox regression analysis and LASSO regression were used to construct the risk prognosis model, and the preliminary verification was carried out. Finally, cell culture and high-resolution gene expression analysis were used to investigate the expression of AQP5 and CTDP1 and their roles in the immune microenvironment. The results showed that AQP5 and CTDP1 were highly expressed in ovarian cancer cell lines and were closely related to tumor immune invasion. The immunomicroenvironment analysis based on GRN showed that they showed a positive correlation with tumor-related immune cells. Through the constructed risk model, AQP5 and CTDP1 significantly affect patient prognosis, suggesting their potential as prognostic markers.