The purpose of this study was to investigate the impact of conjugated estrogen cream, in conjunction with progesterone, on the endometrium, following vaginal administration, and assess the combined dose–effect relationship with progesterone. Initially, bilateral ovaries from mature, female, Sprague Dawley rats were excised to establish a hypoestrogenic (perimenopausal) model. A conjugated estrogen–progesterone combination cream was administered vaginally for a duration of 12 days. Subsequently, this study used pathological sections, Enzyme-Linked Immunosorbent Assay (ELISA) for pharmacodynamic studies, network pharmacology to explore possible signalling pathways associated with the drug and menopausal syndrome, and partial validation using a real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (ICH). The results demonstrate that, relative to the model group, the conjugated estrogen monotherapy significantly increased the uterine weight coefficients (p < 0.0001) and endometrial thickness (p < 0.001) and upregulated the expression of Cyclin D1 and VEGF. Moreover, this treatment downregulated PTEN expression. The co-administration of progesterone reversed these effects in a dose-dependent manner. Overall, the vaginal administration of a combination of progesterone and conjugated estrogen cream demonstrated the ability to mitigate endometrial hyperplasia induced by conjugated estrogen vaginal cream monotherapy. Furthermore, the effect of progesterone exhibited a dose-dependent response.