Abstract: 【Objective】 To analyze the key regulatory pathways in the gill tissues of Sinonovacula constricta under hypoxia stress based on transcriptome sequencing and explore the effects of hypoxia stress on energy metabolism related genes, which could clarify the response mechanism of Sinonovacula constricta to hypoxia stress. 【Method】 Sinonovacula constricta were subjected to hypoxia stress with dissolved oxygen（DO） at 2.0±0.2 mg/L for 12 h（L1） and 24 h（L2）, with a control group（Control） at normoxic conditions（DO 7.0±0.2 mg/L）. Gill tissues were collected for transcriptome sequencing, followed by screening of differentially expressed genes（DEGs） and KEGG signaling pathway enrichment analysis. Real-time fluorescence quantitative PCR（qRT-PCR） was used to detect the relative expression of energy metabolism related genes in gill tissues under hypoxia stress at 0, 4, 8, 12, 24, 48 and 96 h. 【Result】 In the L1 vs Control group, 5445 DEGs were identified, and in the L2 vs Control group, 2980 DEGs were identified. KEGG enrichment analysis showed that 498 up-regulated DEGs in the L1 vs Control group were annotated to 177 pathways, with the top 10 significantly（P＜0.05, the same below） enriched pathways including calcium signaling pathway, cGMP-PKG signaling pathway and C-type lectin receptor signaling pathway. In the L2 vs Control group, 583 up-regulated DEGs were annotated to 224 pathways, with an increase in enriched metabolic pathways compared to L1 vs Control group, including steroid biosynthesis, linoleic acid metabolism, retinol metabolism, ubiquinone and other terpenoid-quinone biosynthesis. Energy metabolism related genes in gill tissues responding to hypoxia stress were screened from DEGs in the L2 vs Control group, mainly involving key regulatory pathways such as glycolysis/gluconeogenesis, TCA cycle, AMPK signaling pathway and HIF-1 signaling pathway. qRT-PCR results showed that with prolonged hypoxic stress, the relative expression of hexokinase gene（HK）, phosphoenolpyruvate carboxykinase gene（PEPCK）, and phosphoglycerate kinase gene（PGK） first increased, then decreased, and then increased again, greatly increased at 4 h of hypoxia stress compared with 0 h, with high expression at 96 h. The relative expression of glucose transporter 1 gene（GLUT1） and enolase gene（ENO） significantly decreased at 4 h of hypoxia stress compared with 0 h, reached the lowest at 12 h, gradually increased after 24 h, and peaked at 96 h with significant differences from 0 h. 【Conclusion】 Hypoxia stress promotes the upregulation of genes in regulation pathways such as glycolysis/gluconeogenesis and HIF-1 signaling pathway, significantly affects energy metabolism in Sinvnovacula constricta. It is inferred that Sinvnovacula constricta maintains energy supply through the glycolytic pathway under hypoxia stress, and genes such as PEPCK, HK, GLUT1 and PGK are involved in energy metabolism regulation and hypoxia stress response.