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BACKGROUND Shrimp is one of the most popular marine foods consumed throughout the world and the freshness is the crucial indicator for consumers. However, the flesh quality degradation of shrimp during waterless live transport has been observed and the underlying mechanism remains unknown. RESULTS The present study aimed to clarify the biochemistry mechanisms of flesh degradation with integration of quality evaluation, metabolic profiling, and histopathological analysis. The flesh quality indicators such as water holding capacity, protein and lipid contents, amino acid composition, and myofiber components degraded with the prolongation of combined stress. In addition, the metabolites including gamma-aminobutyric acid, Val-Ala, Trh and derivatives of carnitine, phosphocholine, and prostaglandin all reduced significantly under combined stress (P < 0.05). Furthermore, KEGG analysis discovered the enrichment of neuroactive ligand-receptor interaction and estrogen signaling pathways, indicating the involvement of neuroendocrine in stress response. Moreover, architecture impairment in hepatopancreas tissue verified the accumulation of metabolic disturbance. CONCLUSION Altogether, these findings indicate that neuroendocrine system mediates the flesh degradation of L. vannamei during waterless transport by disturbing the biochemical metabolic pathways and inducing architecture impairment on myofibril components. This article is protected by copyright. All rights reserved.