Sinibrama taeniatus is a rare and small economic fish which is distributed in the upper reaches of the Yangtze River. S. taeniatus can reproduce twice a year in the wild, while the reproductive cycle of S. taeniatus reared at the temperature of 26 °C is only 14 days. Low temperature is a major factor limiting the reproduction of the fish in the wild, especially in winter. We found that the low temperature of 11 °C significantly inhibited the ovarian development of S. taeniatus. To explore the effects of low temperature on ovarian development, the female S. taeniatus after spawning were reared at a low temperature of 11 °C (LT groups) for two weeks, and the fish reared at the temperature of 26 °C (OT groups) as control group. We compared the ovarian development of the LT groups and OT groups. The morphological and histological results showed that the ovarian development was inhibited in the LT groups and that the oocytes were underdeveloped and degenerated. Besides, the atretic follicles were observed in the ovaries of the LT groups. The results of enzyme-linked immunosorbent assay and qPCR showed that the secretion of FSH and DHP, and the gene expression of fshr, lhcgr, pgr, esr1, and ar were significantly inhibited by the low temperature. Transcriptome sequencing results showed that the differentially expressed genes were significantly enriched in steroid hormone synthesis, cell growth and proliferation, apoptosis, and autophagy pathways, indicating these pathways were affected by the low temperature significantly. The expression of genes involved in pro-apoptosis (i.e. bax, tnf, and tp53) was up-regulated in the LT groups. However, the expressions of genes involved in steroid hormone synthesis, oocyte development, cell growth and proliferation, and anti-apoptosis, viz., StAR, cyp17a1, hsd3b, cyp19a2, hsd17b1, vtg1, zp4, mmp9, mmp15, ccni, cdk16, igf1r, egfr, nobox, and bcl2 were significantly down-regulated in the LT groups. It suggests that the low temperature may inhibit the synthesis and action of reproductive hormones, limit oocyte growth and proliferation, and promote autophagy and apoptosis of follicles which results in follicular atresia. It provides a theoretical basis for conservation biology and artificial reproduction of S. taeniatus.