Large yellow croaker (Larimichthys crocea) is an important marine fish species. The reduction of salinity can promote fish growth and reduce the risk of Cryptocaryon irritans infection. This study evaluated the effects of low-salt acclimation on oxidative damage and transcriptome in the liver of L. crocea under hypo-saline stress. Fish with an average weight of (52.46±1.47) g were pre-exposed to salinity 25 or 20 for 7 d, and subsequently were subjected to salinity 10 for another 24 h. The results indicated that hypo-saline stress increased reactive oxygen species (ROS) and lipid peroxidation (LPO), low-salt acclimation had no effect on ROS and LPO. Interestingly, low-salt acclimation with hypo-saline stress reduced ROS and LPO when compared with hypo-saline stress, suggesting low-salt acclimation alleviated hypo-saline stress induced oxidative damage. A total of 356, 478 and 484 differentially expressed genes (DEGs) were obtained from low-salt acclimation group vs. control, hypo-saline stress group vs. control, low-salt acclimation with hypo-saline stress group vs. hypo-saline stress group., respectively. The results of GO functional enrichment and KEGG pathway enrichment showed that DEGs were significantly enriched in GnRH signaling pathway, PPAR signaling pathway, apoptosis, MAPK signaling pathway and Toll-like receptor signaling pathway, indicating low-salt acclimation improved hypo-saline stress tolerance of large yellow croaker by regulating ion and material transport, lipid metabolism, apoptosis and nonspecific immunity. Those findings revealed the regulation mechanism of low-salt acclimation enhanced hypo-saline stress adaptation, and also provided scientific basis for factory farming and inland farming of L. crocea in fresh or brackish water.