Hypoxia is a critical, but frequently overlooked problem, which commonly exists in Chinese mitten crab rearing. However, little information is available on the molecular mechanisms of the detrimental effects of hypoxia in this species. In the present study, crabs were subjected to acute hypoxia stress (DO 1.0 mg/L), followed by reoxygenation (DO 6.8 mg/L). Hepatopancreas from five groups of crabs (three to four crabs per group), including normoxia, hypoxia for one and six hours, and reoxygenation for one and 12 h, were used for transcriptome sequencing. The pooled total RNA of all samples were utilized to reconstruct a reference transcriptome with PacBio RS II sequencing, obtaining 49.19 G clean data, with a mean length of 2,180 bp. Seventeen cDNA libraries were constructed and sequenced to identify differentially expressed genes (DEGs) among the different samples (FDR < 0.05 and |log2 fold change| ≥1). A total of 103 and 251 DEGs were identified when exposed to hypoxia for one and six hours, respectively. Totally 462 and 673 DEGs were identified during reoxygenation at 1 and 12 h, respectively. Among these DEGs, two transcripts with complete ORFs were identified to encode hypoxia-inducible factor 1 (Es-Hif-1α/β), which is a transcriptional activator of various genes correlated to the cellular adaptive responses to hypoxia. Es-Hif-1a/β expressions were significantly upregulated when exposed to hypoxia treatment, and no significant difference was observed for Es-Hif-1α between hypoxic treatment for 6 h and reoxygenation. The significant KEGG enrichment revealed that the DEGs under hypoxia were mainly enriched in “PPAR signaling pathway”, “Gap junction” and “Phototransduction-fly”. Compared with crabs in normoxia, even with 12 h of reoxygenation, the hepatopancreas transcriptome under hypoxia remained severely affected, implying its adverse effect on growth and development, or increased susceptibility to diseases.