In order to explore the adaptability of Cyprinus carpio var. qingtianensis (Paddy Field Carp) to acute dissolved oxygen changes in paddy fields, Our treatment conditions simulated the acute hypoxia and reoxygenation environment according to the tolerance parameters of Cyprinus carpio var. qingtianensis and the daily situation in the local paddy field water environment, and transcriptome analysis was conducted in brain tissue samples from normal oxygen control group(CB groups), hypoxia stress 6 h group (HB groups) and reoxygenation group(RB groups) by RNA-seq technology. The results showed that there were 1 094 differential genes in the library of the HB groups and the CB groups, of which 730 were up-regulated and 364 were down-regulated; the comparison of the RB groups and the HB groups library revealed 2 288 differential genes, of which 803 were up-regulated and 1 485 were down-regulated; the RB groups library revealed 201 differential genes, of which 80 were up-regulated and 121 were down-regulated compared with CB groups. Further, GO and KEGG analysis indicated that acute oxygen changes were involved in multiple biological pathways, mainly glycolysis/gluconeogenesis, HIF-1 signaling pathway, mTOR signaling pathway, VEGF signaling pathway and insulin signaling pathway. Finally, 6 differential genes were verified in the glycolysis/gluconeogenesis and related pathways by RT-qPCR experiments, which confirmed the reliability of the transcriptome sequencing results. These results provided basic molecular biology information for studying the physiological regulation mechanism of Cyprinus carpio var qingtianensis in the environment of acute changes in dissolved oxygen.