Female germline stem cells (FGSCs) can self-renew and differentiate into oocytes, replenishing the depleted primordial follicle pool. The traditional Chinese herb, Cistanche deserticola Y.C.Ma, has been used to treat infertility for centuries. Cistanche deserticola polysaccharides (CDPs) are its main active ingredients. In the present study, an animal model of premature ovarian failure (POF) was established to investigate the protective effects of CDPs on the ovary. Ovarian tissue structure and function were assessed after treatment with CDPs, with emphasis on FGSC activation in the ovarian cortex. FGSCs were isolated from newborn mice and treated with CDPs. The morphology, proliferation, expression of stemness, and differentiation markers were evaluated to determine the role of CDPs in promoting FGSC differentiation in vitro. Furthermore, bioinformatics screening identified small mothers against decapentaplegic homologue 9 (Smad9) as a key factor in the signaling pathway. We established a Smad9 differentially expressed cell model using gene modification. We then evaluated changes in the expression of cell stemness maintenance and differentiation ability octamer-binding transcription factor 4 (Oct4), mouse vasa homologue (Mvh), stimulated by retinoic acid gene 8 protein (Stra8), and synaptonemal complex protein 3 (Sycp3) and Smad family markers (SMAD1, SMAD5, SMAD9, SMAD1/5/9, and p-SMAD1/5/9). This approach aimed to verify the molecular mechanism by which CDPs regulate FGSC differentiation through the BMP-SMAD family signaling pathway, ultimately supporting its potential role in improving ovarian function.