Abstract: Large yellow croaker (Larimichthys crocea) is an important marine economic fish in China, however, it faces challenges such as insufficient aquaculture water, severe water pollution, and frequent occurrence of diseases. Expanding cultivation from the inner bay to the outer sea can address these issues, but varying water salinity across sea areas poses a hurdle. Thus, it is necessary to understand the impact of salinity changes on fish physiology. This study aimed to compare how high and low salinity affect energy metabolism and mitophagy in the liver of large yellow croaker and elucidate the underlying mechanism. Fish weighing (53.46±1.47) g were obtained from Fufa Aquatic Co. Ltd. (Ningde, China) and randomly placed in 400 L fiberglass tanks (9 tanks) with seawater salinity at 12, 25 or 40. This setup was maintained for 1d, 3d and 7d, with three replicates for each salinity group. Measurements included oxidative damage markers (radical oxygen species (ROS)), energy metabolism indicators (adenosine triphosphate (ATP) and lactate contents; pyruvate kinase (PK), lactic dehydrogenase (LDH), succinate dehydrogenase (SDH), malate dehydrogenase (MDH), ATP synthase (F-ATP), carnitine palmitoyl transterase-1 (CPT-1), acetyl-CoA carboxylase (ACC) and adenosine 5’-monophosphate (AMP)-activated protein kinase (AMPK) enzyme activities), and mitochondrial autophagy indicators (microtubule-associated protein light chain 3 (LC3α), PTEN induced putative kinase 1 (PINK1), Parkin, mitofusin 2 (Mfn2) and forkhead box class O3 (FoxO3) gene expression levels). The results showed that tricarboxylate cyclase enzyme (SDH, MDH and F-ATP) activities and mitophagy gene (LC3α, PINK1, Parkin, Mfn2) expression levels in the high-salt group were significantly higher than those in the low-salt group on day 1, indicating that increased energy consumption and enhanced mitophagy to cope with early high-salt stress. The high-salt group increased fatty acid β oxidase enzyme (CPT-1) activities, and reduced F-ATP activity and LC3 α gene expression levels on day 3, resulting in increased lactate and ROS contents. F-ATP activity and LC3α gene expression levels in the high-salt group were lower while ROS and lactate contents and acetyl ACC activity were higher than those in the low-salt group on day 7, suggesting a shift toward decreased aerobic metabolism, reduced mitophagy, and increased anaerobic metabolism, leading to insufficient energy supply, loss of mitophagy function, and exacerbated oxidative damage. Furthermore, gene expressions of AMPK and FoxO3 positively correlated with mRNA levels of energy metabolism and mitophagy related genes, respectively, indicating that AMPK and FoxO3 played important roles in regulating energy metabolism enzyme activities and mitophagy gene expressions during the salinity stress. In conclusion, research results highlight the differences in the effects of high and low salinity on energy metabolism and mitophagy in large yellow croaker. These findings provide basic data for formulating salinity regulation plans and selecting suitable aquaculture water bodies for large yellow croaker.