Objective To investigate the causes of infertility and its pathological mechanism in female SD rats with spontaneous dwarfism (short stature rat, SSR). Methods Adult wildtype and SSR female SD rats were used in this study. A vaginal smear was used to observe changes in the motile cycle. Ovulation promotion was compared using the simultaneous estrus supernumerary ovulation method . Ovarian and uterine weight and body weight, and ovarian and uterine indices were measured. AMH, E2, FSH, LH, and FSH/ LH levels in serum were measured. Transcriptome sequencing of ovarian tissues was performed to analyze gene expression differences. Results No abnormalities were observed in the estrous cycle of SSR female rats. The body weight of SSR female rats was significantly lower than that of wildtype rats, and their ovarian and uterine indices were significantly higher than that of wildtype rats. The mean number of ovulations was significantly higher in wildtype rats than in SSR female infertile rats (P< 0. 001). Serum AMH (P< 0. 01) and E2 (P< 0. 05) levels were significantly higher in wildtype rats than in SSR female infertile rats, and serum levels of FSH, LH, and FSH/ LH (P<0. 05) were significantly lower in SSR infertile females than in SSR infertile rats, while PROG showed no significant difference. Transcriptome sequencing yielded 250 differentially expressed genes, including 190 upregulated and 60 downregulated genes. p53 signaling pathway and cytokine-cytokine receptor interaction. The MCC, MNC, EPC, and degree calculations of the CytoHubba plug-in were used to screen the top 10 significant nodes. The intersection was used to finally obtain nine hub genes, namely Cxcl1, Cxcl2, IL1a, IL1b, Cd80, Mmp13, Mmp8, Fgf3, and Ptgs2. Conclusions Infertility in SSR female rats may be related to a decreased ovarian reserve function and poor ovarian response. Cxcl1, Cxcl2, IL1a, IL1b, Cd80, Mmp13, Mmp8, Fgf3, and Ptgs2 were associated with infertility, laying a theoretical foundation to further explore infertility mechanisms.