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Hypoxia has become a common phenomenon in aquatic environments. Golden pompano (Trachinotus blochii) are sensitive to fluctuations in dissolved oxygen concentration and are seriously affected by hypoxic stress. When facing hypoxia in aquaculture areas, it may be effective to alleviate the adverse effects of low oxygen by increasing dissolved oxygen through physical and chemical means. However, it is not known whether different reoxygenation rates have different physiological consequences. In this study, we utilized RNA-seq and miRNA-seq to investigate the effects of various hypoxia and reoxygenation treatments: normoxia, hypoxia, rapid reoxygenation (RRG; dissolved oxygen [DO] recovery within 10 mins), and gradual reoxygenation (GRG; DO recovery within 3 h). Under hypoxic conditions, the miR-130b-5p∼IDH3pair was involved in the regulation of the TCA cycle and activation of HIF-1α expression in response to insufficient oxygen levels. Additionally, in RRG, under the regulation of the miR-132–5p∼PGAM, miR-8485∼LIPA, and miR-212–5p∼GAPDHSpairs, the energy supply came to increase relative to hypoxia. In GRG, the miR-130b-5p∼IDH3pair regulated metabolism, which returned to the normal level. These findings provide new data for clarifying the metabolic regulatory pathways of golden pompano during hypoxia and reoxygenation processes.