| Sinibrama taeniatus is a kind of rare and small economical fish which distribute in the upper Yangtze River. S. taeniatus can reproduce twice a year in the wild, while the reproductive cycle of S. taeniatus reared under the temperature of 26℃ is only 14 days. Low temperature is a major factor limiting the reproduction of fishes in the wild, especially in winter. We found that the low temperature of 11℃significantly inhibits the ovarian development of S. taeniatus. To explore the effects of low temperature on ovarian development of S. taeniatus, the female fish after spawning were treated with a low temperature of 11℃ (LT groups), and the fish reared under the temperature of 26℃ (OT groups) severed as control groups. 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 RT-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 differential 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. The expression of genes involved in pro-apoptotic (i.e. bax, tnf, and tp53) was up-regulated in the LT groups. However, the expression 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 suggested that the low temperature may inhibit oocyte growth and proliferation, and promote autophagy and apoptosis of follicles which resulted in follicular atresia.